Kinda makes me wonder if GPU slots should be on the other side of motherboard.

Didn't Gamer's Nexus or LTT show a board like that a few years ago?

The issue there is probably case form factors in the target market.

If you produce a great solution, but everyone has to source or build a custom case, you probably aren't going to sell many.

I think there are some cases with a daughterboard containing the GPU slot in a separate “heat compartment” from the rest of the case. The PCIe is extended over to that board so everything else should still be standard. It probably adds some small latency, though.

Signal path latency is orders of magnitude lower than PCIe protocol latency.

I recall one with the CPU socket on the back of the board, maybe that's what you're thinking of? IIRC both LTT and GN did videos about it