I recently bought a Corsair 5000D Airflow, pretty much the same case as the 5000X minus the RGB and with better airflow, and I also bought a Z690 Classified. Unfortunately, I am unable to use the front-panel USB connectors due to the exact reason you mentioned, prompting me to buy a USB extension cable to run from the rear I/O ports. Plus, I had a heck of a time connecting the 24-pin even with individually-sleeved cables from CableMod. I had to remove the top rubber grommet because the 24-pin kept rubbing it out of place when connecting it. As far as my GPU goes, I haven't had any issues with it. It's a 3080 Ti FTW3 with an EK water block I attached, so it's not as bulky as a 3090 Ti. When it comes to my PSU, it's also a SuperNOVA 1000 T2, and I removed the hard drive bay as one of the first steps I took prior to installing it. All my storage is m.2, so there's no point in having the bay there except to make managing the "rat's nest" of PSU cables that much more annoying, but your mileage may vary depending on storage type.
 
Both Corsair and EVGA made a good product in their own regard, but the two don't seem to be highly compatible in this situation. The Corsair 5000 series could stand to be 1-2" longer from front to back, as evidence of our situation with the USB connectors as well as me having to buy a narrower 360 radiator to fit the side intake area. Corsair definitely should have provided more exact product dimensions instead of something along the lines of, "fits up to a 360 radiator." Yeah, it fits a 360, but only a 120 mm wide one. The one I had and wanted to use is 133 mm wide, so it plain ol' wouldn't fit. That's something I found out the hard way. And, EVGA should reconsider the parallel connectors, especially for eATX motherboards. I've had eATX boards before and even replaced one with the the Z690 Classified, but the Classified is easily the longest board I've owned. I didn't think it was going to be as big an issue installing it as it wound up being, and it's thanks largely to the parallel connectors for the 24-pin and USB. Had the connectors been perpendicular to the board like 99.99% of all other motherboards, we wouldn't be having this discussion. At least I was able to connect my fan hub to the USB 2.0 header with less of a headache, but even that was a tad difficult given the parallel connectors for it as well as the shroud that covers it. The Z690 Classified has a sleek design, but it's not a very installer-friendly or case-compatible motherboard.

B0baganoosh
The 5000X (and 5000D) is a very nice case, but definitely has some limitations when it comes to these slightly oversized motherboards and trend of super-chonky GPUs.
 
I think it was Nereus (and a couple others) on here posting about issues with that case and their z590 builds as all the down-facing right-angle connectors were aimed straight at the PSU shroud and couldn't be connected without some serious kinks in the wires. The z690 boards are even larger, especially where they extend to the right, so I can definitely see how that'd be a tight fit.
 
The only solution I can see for cases these days is to shift the shape and size and build in capacity for external radiators. At least until CPU and GPU thermals come back down into sane levels. Right now we're headed at ludicrous speed straight to Dutch oven status.
 
Also, I had a similar problem with my be quiet! Dark Pro 900 (v1), but they left an essential gap between the power supply shroud and the motherboard: 

I have things connected to the bottom plugs, and I did not remove the power supply shroud to do it. I hugged my computer with one hand reaching behind to carefully push the connector up and the other holding two fingers over the shroud in this picture to sort of aim by feel. It was...not fast...or easy. I didn't want to bend any pins, so I just went real slow and made sure alignment was good before pushing on it.
 
Of course it would be a little higher if I didn't have a big radiator in the top of the case in push-pull, as this case allows you to raise and lower the motherboard tray, but then things would run hotter than they already do.

Components are definitely running hotter and hotter these days. That’s why I opted for the 5000D Airflow. It’s definitely helped with thermals compared to the Fractal Define R6 I was using previously, but the Corsair 5000 series definitely has its quirks. My impression is that it has a more proprietary design to it, with Corsair wanting or expecting customers to buy their parts to use with these cases. That’s actually what I wound up doing with my side intake radiator. I had a Hardware Labs (HWL) 360 that I intended to go there, but I quickly learned it wouldn’t fit due to its 133 mm width. I would have gone with a HWL L-series rad to replace it, but they’ve been sold out for a while, so I bought a Corsair 360 that is exactly 120 mm wide. At least it’s made by HWL. Otherwise, I stand by my statement that EVGA should rethink their connector orientation, as it’s currently not conducive to installing in a typical case. Not even ones that claim to support eATX motherboards. Then again, there is no standard for eATX dimensions, so it’s all on a case-by-case basis and further suggests reorienting the connectors would increase compatibility.

milkman76
Hello -- does anyone have a Corsair 5000x RGB case?

If so, when you installed your z690 classified into it, how did you connect the board's USB 3.2 g2 header to the case's internal USB cable without the metal fan cowling for the tray fans smashing it and not closing properly? The USB 3.2 g1 header comes with a right angle adapter, and it doesn't impact the cowling. The g2 header is the issue, and has no right angle adapter.

I can remove the entire metal fan cowling / cable tray, but then the fans I'm installing won't put air pressure on the rear/tray part of the motherboard and I won't really be able to use 2 or 3 of my fans. Does anyone have this experience? If so what did you do??

Thank you.


Edit: it's much worse than just not being able to fit the gen 2 USB 3.2 header along with the tray fan cowl.

In order to install my EVGA supernova 1000 t2 psu, I had to remove the 2x HDD bay that is next to the PSU. It totally blocks the cables coming from the PSU and there is no way to fit it.

And, I've just gone to install my new 3090ti, and I've found that it hits the tray fan cowling also, making it impossible to install this GPU along with the regular case format.

Word to the wise -- if you buy the 5000x case, don't plan on using your double sized GPU or the really nice (on paper) tray fan system that pushes air along the back and through the SSD area if you have any EATX motherboard with the vertical-facing USB header. I'm honestly not even sure if a single thickness GPU would fit into this case with the fan cowling installed.

I'm going to go yell at Corsair. This is 100% a Corsair issue, and it should have been clear on paper.

 
Fully agree with you, the 5000 case from Corsair is a bit too small for E-ATX and bigger GPU.
I spend some hours to bring everything together, it works fine now and is ok for me as it is.
I installed three fans in front, three at the side, one in the back and two at the top.
 
Send you over some pics so that you get an idea/ impression, you can see them here:https://photos.app.goo.gl/NQsPjPQBKb38GBy3A

milkman76
I just got an email back from Corsair on this case -- they apologized and said "we built our case before the z690 was released". 
 
Yeah Ive got my system running well, and Im pleased with cooling and fan placement even though the fan cover is not installed. It worked out.
 
The only thing Im struggling with is the HDD bay. I was going to use this machine to run 2 big disks in raid, and now I will probably have to find a separate, more costly way of solving that.  

Sounds like a cop out to me. Yeah, the 5000 cases were designed prior to the Z690 Classified, but that still doesn’t account for the need for an exact 120 mm-wide radiator for the side intake. Had they made the case just an inch or two longer, it’d have accommodated a wider variety of radiators as well as the Classified.