Couple thoughts, for standoffs, the Meshroom S is entirely 6-32 thread based, not a hybrid 6-32/M3 like the Meshlicious is. You'd best be off buying 6-32 standoffs, but M3 may work, but may not secure that well as M3 is smaller and a different pitch which could lead to stripping the thread. The Meshroom S comes with enough extra standoffs to move the GPU (user manual above shows it again).
If you keep the GPU in the lowest and closest position to the spine, you should have enough standoffs to Frankenstein a motherboard standoff mod form what's included with the Meshroom S. However, if you want to move the GPU at all, or you want your standoff to look a bit nicer, I'd recommend buying a 1inch (or 25mm) long 6-32 Male to female or female to female standoff for it. I used this, but it's from the US site with a couple of the 6-32 screws included with the case on each standoff. As you mentioned though, you may not be able to do the motherboard standoff mod if you need the case in 4-slot mode for your 4090. I feel like the answer for the 3 vs 4 slot 4090 question should be findable in this subreddit or SFFPC.
As for M.2 drives, I have a be quiet! BZ002 MC1 M.2 SSD heatsink on my rear NVME SSD and it's no warmer than the front NVME SSD so I don't think it matters too much. That being said, I have the mobo standoff mod, so there's room for airflow. If you can't do this, I'd put the less-used SSD on the rear, which will probably be the smaller one per your post.
The Meshroom is definitely 6/32
I got some standoffs from Amazon.com
And 6/32 UNC screws off ebay
https://www.amazon.com/gp/aw/d/B07K35HYR3?psc=1&ref=ppx_pop_mob_b_asin_title
The do different lengths and also hexagonal steel ones as well
Don't use 3m, that's what the old meshlicious was