Neat project! I’ve done a couple (basic, consumer, no modifications of the case) mini itx builds and always wished I could get the GPU out of the case. Stick the hot thing out in the world, where it has infinite airflow, seems like the most obvious thing to do, but it really isn’t catered to well enough…
Links have to be very smart & capable of self training in modern PCIe to perform at the speeds they do: they have link equalization. So there's incredible diagnostics builtin.
As for active cables, Marvell just announced Alpine P, which is a PCIe6 retimer that capable of working in active electrical cables (and also active optical cables!). I don't know if they buffer data or not - if so it would be a small amount of data I'd expect - but they do receive & retransmit. https://www.servethehome.com/marvell-extending-pcie-gen6-rea...
Cable extenders are known for messing with signal integrity. Flipping bits over long wires takes a while. ML training seems (I could definitely be wrong here) less latency sensitive than classic GPU applications, like gaming. But it does want the bandwidth. Could there be room for an active cable with repeaters? Does anyone make a cable with, like, little flip-flops in it? Can an extender act as a little buffer or pipeline or something like that?
Cunningham’s law: activate!