As well as standard forge fluids (which can be piped in/out of a compact machine just fine), Mekanism also has gases, and ore slurries (which oddly, aren't considered a standard fluid). These can only be piped around via either Mekanism's pressurised tubes, or EnderIO's gas conduits.

In the case of gases, it's possible to get them into a compact machine with a workaround (using Rotary Condenstrators from Mekanism to convert between fluids and gases as required), albeit this introduces a bottleneck in processing pipelines. In the case of ore slurries, as they cannot be converted like gases can, there is, to my knowledge, no way at all to get these in or out of a compact machine.

Would it be possible to natively support transmitting these through the interfaces of a compact machine?

EnderIO's support may be a useful reference.

I've started working on this in my fork of this repository. Can't say I've done MC mod development before, but if I do manage to get it working, I'll send through a PR.

Merged. Thanks a lot. Awesome pull request.