12VHPWR is the gift which keeps on giving!
If it is that sensitive to bending, then how wide do cases need to be? I guess monsters cases like be-quiet! 900DX or similar which are 327mm wide seem to have tons of space beyond the PCIe width although I exact space is not in the spec but lit looks like the designed it so a vertical GPU could fit there. Not sure I'd trust a 5090 with a PCIe 5.0 x16 ribbon cable though.
A rough pixel counting has say that case hasa about 70mm past the PCIe - so the 40mm no bend advice would leave 30mm to bend it 90° which IMO is still tight! So does this mean a 400mm wide case is the "safe" bet for a 3090? Not many cases that wide.
Ironcically if 12VHPWR's reason for existing is mainly cosmetic, then most the fixes for it seem to look pretty naff!
Reading the OP, for diagnostics after stock I would have tried underclocking / setting a lower power profile for both the CPU and GPU to try and get a handle on it. I mean even if that worked, that doesn't get you all the way: The Seasonic 1600W should be really good but I'd still try eliminate it so I'd next try GPU at the underclock which was stable and start crank the CPU instead just to see if there is a magic wattage where everything fall over (so mostly blame the PSU). And similar processes. Must be pretty frustrating to have bought such a high-end system then spend weeks/months diagnosing problem.
Well, that would have been my approach but how 12VHPWR behaves with underclocking is an unknown.