Nice find on those B2Bs! I tried locating them myself a couple of years ago with the same problem you found. I did suggest a simple wire loom or FPC style connector could be produced by Pi-Top as an accessory/adapter for connecting other SBCs’ GPIOs to the hub but that didn’t come to fruition either.
As regards Libre Computer SBCs, I can now confirm that I was able to successfully fit the Alta model in the pi-top [3] chassis, with the hub appropriately sited (HDMI and 3.5mm A/V ports lined up just fine) and, after gently teasing the heatsink off the CPU and RAM (be careful as it’s stuck on quite firmly with adhesive tape), I was able to fit the cooling bridge from the GPIO pins to the B2B connector on the hub.
I have yet to try actually running an OS on this board as Libre Computer are supposed to be releasing an update later this month, I think, for greater ability to simply run whichever vendor’s aarch64 images (Fedora, Nix, Ubuntu etc.) without the end user having to modify them first.
But the fact that we are finally able to correctly fit a decent, USB3 capable SBC with more than 1Gb RAM in the pi-top [3], without modification*, is great!
*I don’t count removing the heatsink as modification
N.B. I have not yet tried this assembly with an eMMC fitted beneath the Libre Computer so it’s possible that might change things.