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Will putting GPU in second slot affect performance on Sabertooth x79 with a 4930k?

Level 7
Specs first:

Silverstone FT-02 Fortress Black
ASUS Sabertooth x79
Intel 4930k
MSI GTX 970 Gaming
Corsair H100i liquid cooler
Corsair Vengeance 32GB (4x8GB) DDR3 1600 MHz
EVGA 860 Watt power supply

I have an issue involving the size limitations of my Silverstone FT02 and a RTX 3090 I'll be adding in a few weeks. Those who are unfamiliar with Silverstone cases, it has a design build where the mobo is rotated 90 degrees for a cooling system that pushes air from the bottom up top. However, because of that my current 970 at 277mm length is already butting up against my Corsair H100i radiator which is also sitting on top of the three 180mm fans pushing air from the bottom of the case. So because of this I'm gonna have to make some serious modifications in order to accommodate the 3090 at 300mm. Btw I'm using this primarily for work not gaming fyi in case those of you questioning why this I'm going this GPU, but also to add I’m a 3d artist and I’m gonna use the GTX 970 to drive 3ds Max viewport performance while using the 3090 for RT rendering. It helps lessen the load so my workflow doesn't slow down in this configuration.

With all that said, short of getting a new AIO cooler so the 3090 can fit in the first slot, I consulted the manual to see if I can use the Slot 4 for the 3090 and slot 1 for the 970 since both lanes are x16 speeds, and because the 4930k is 40 pcie lanes I should technically be fine, correct? I want to be sure because in the following page of the manual it says that it recommends slot one for single VGA card mode for better performance. Now if push comes to shove and I'm unable to squeeze both the 970 and 3090, I will stick with just one GPU anyways but I still need clarification if slot 4 will still give me the same performance as slot one because there's no way I'll be able to move the radiator at all and fit the 3090 in slot one at the same time so my only option is slot 4 or get a new cooler.

Assuming this all works fine with both GPU's, my other question is will I have to make any modifications to my bios to assign the 3090 in the second slot as the primary/master gpu or will it automatically be assigned after installing the drivers? I'm sorta confused in this regard.