B0baganoosh
That is definitely interesting and sounds like a BIOS bug to me. I wonder if on Auto, it they were enabled, which was causing an issue with legacy boot (I think those require EUFI to work)...then when you disabled and went back to "auto" they were still disabled. So "auto" just left them in some previous state instead of switched them based on the other settings and hardware. Just a theory. If you leave them manually set to disabled, does it continue to boot correctly or was it just an intermittent chance?
Similar to your plan, I bought a G6900 trying to test out the 7F code issue I was having and it worked perfectly fine (compared to the 12900k I couldn't get to boot right 100% of the time).
As for comparisons with the Dark boards, I think the Classified boards are just a little thinner with a couple less copper layers so they might flex just a little more, which makes them more susceptible to uneven tightening. You're probably right that it isn't the issue, but it is something physically different between those boards and another reason I bought an aftermarket back-plate for behind the motherboard to stiffen things up on my z690 Classified. I'm going off memory from z690 announcements (can't remember z790 honestly) so I could be mistaken there.
Yeah i think I'm going to reflash the bios next and see if that helps. Also try other bios switches.
The other weird thing is originally when i first went from uefi to legacy, i couldn't boot without also setting above 4g and rebar to disabled. After i DID get it to boot with those 2 disabled and legacy boot, i randomly had D4 boot failures even after multiple successful posts. This time though, i was able to hit reset and it posted the 2nd time. This is in contrast to earlier when i first set it to legacy it would get stuck on D4 until bios wipe and reboot/power off didn't fix it.
Only other thing i could think of is the Z790 classified doesn't like my evga 980 ti classified. I've had other weird issues with it on my X299 Dark where there's no display out until Windows successfully posts. (No bios screen, etc) But will display perfectly after Windows boots and Nvidia drivers come up. There i had to use an old 8400 gs and it would display just fine. I'm starting to think it also could be an issue with loading the 980 ti upon post.