Yeah, I did some research again. Making an actual motherboard is like 200k or more USD. Even if you bring it down to 100k, you can still buy like 4 really powerful double CPU servers (256 core, 512 threads) with that. It doesn't make any sense to create your own one, unless you are actually in the business of motherboards. I mean, yeah, you will have constraints, but it's actually not even a problem, unless you are trying to build a neutrino-atomic computer that is a size of flash memory stick and have the power of RTX 4090, did I say that it would be able to fly on its own too?
Now it's another question if you can bring the cost down to 25-50k somehow, that would actually be viable. But bringing the cost down 8-fold, is a lot to ask. Manufacturing these, is not a problem, it's not that expensive either, carrier-board + the rest of the functionality will cost you ~1000-1500$ total a piece, even in small volumes. But the cost of the design, that's where the problem lies. While it's non-repeating cost, you would want to design all kinds of motherboards and improve them iteratively, which is why it has to be low.
So yeah, I will just buy a carrier board from lattepanda or something, when I need custom work. Otherwise, it's even more fun, just buy a server mother board with many PCIe ports and you can do A LOT with them. Additional NVMes or something else, you can design it in such a way that it will have flexible busses going towards places you need etcetera.
Thank you for your advice.