So are you saying you paid for the 10980XE but received the 9980XE instead?  If so yes the 2 are pretty much identical except for a few newer features in the 10980XE.  If you got a 9980XE for around $1000 then it was still a great deal but on the other hand if you ordered the 10980XE thats what you should have received. Amazon was having a lot of issues where they had the 10980XE listed with the wrong SKU and people were receiving the wrong products.  However its then hard to prove that unless you took a video of the unpackaging of the item.  I have had both the 10980XE and the 9980XE and was able to pretty much get the same results from both. 

Well if you receive the 9980XE for that price its a great deal. 

Very good, you got a great deal on the 9980XE. 

Clock-for-clock, the 9980XE is faster than the 10980XE. The 10980XE has in-silicon spectre mitigations added which slowed it down a bit clock-for-clock. So when comparing performance and features, it really depends on the clock speed used and how much you value spectre mitigations.

Congrats on this upgrade. Getting an AIO cooler to replace the air cooler when be beneficial. 

I Hope you get an Answer, I would Love to know the technology behind this, the facts about X299 and X299X, the difference between Cascade Lake ready, and Cascade Lake Capable. The Article says”
Intel^®'s Latest Platform Unlocks Unbelievable Performance

• Supports up to 36 CPU threads (18-core)
• Up to 44 PCI-E 3.0 Lanes

 
But it’s hard to sell something promising 48 lanes, if the Board will only do 44. Which is why I did not let it bother me that I got the 9980 instead of the 10980, Figured I was NOT getting the other 4 lanes anyway, But I do NOT really know for sure, A Technical explanation would be great to read, and fun to learn.... I would imagine the traces would already have to be built into the layers on the mother board, unless it preforms some switching function, based on demand. And the additional Lanes can't go anywhere, Unless there is a Path for them to get to where they need to go, and a Bios Version, to tell them how to get there; and with them both being Unlocked Version, I imagine, they both end up at the same speeds, based more on the cooling you give them, more so that the generation they are. Anyway that's My Understanding, But it's all assumption, not Fact.

It all depends on silicon lottery, the 10980XE could have been even worse in OC potential than the 9980XE.

I would not be happy with the outcome of that deal. If I received an i9 9980X when I paid for an i9 10980X I would advise them they sent the wrong CPU and ask if they can provide a replacement either in RMA or when they come in stock and you return the one they sent you. How are you going to explain that to Intel if you have to provide proof of purchase? They are not the same, if you say nothing you passively accept the deal, if you initiate... you open room for negotiation. I would see if they could discount your purchase if you want to accept this deal. You paid for that when it was in stock. Just because things are ridiculous expensive right now, does not mean you should just accept that deal. A few months back I could have had a i9 9940X for 600, a i9 9820X for 300... later on found a i9 9900X for 470. I see deals on that kind of stuff all of the time.  

You are right about the "X299X chipset" it's not a new chipset, it's just Gigabyte's designation to show it supports the added PCI-E lanes and upgraded memory controller. MSI didn't do the same, they made a few new ones too.

Yes there is almost no difference between the two chips when it comes to performance. My 10980xe I can get to pass cinebench R15 at 5.1ghz if the temps allow but I have seen 9980xe chips that can even do that so it comes down to silicon lottery. You can overcome the spectre and meltdown security patches with a XOC Bios it seems but running like that for daily use is risky.