The USB module is just a power connection for things like controllers, etc that can be powered over USB. It doesn't pass any signals.
The problem with interfacing AE to anything else is that the AE likes to see a very specific range of incoming voltages, namely 0 - +5V...and this goes for ALL incoming signals, whether they're CV, mod, trigger, gate, or audio. This means that you either have to use a buffering module such as the AE 4I/O or a Soundmachines Nanobridge to constrain and offset signals properly. Plus, you have to establish a groundplane between the AE and other devices, sort of the same thing that's needed with a banana-patcher such as the Kilpatrick Phenol, Serge format gear, et al. Without that last detail, you won't have a signal return and your connections between the AE and whatever it's hooked to won't happen.
Actual Buchla format (as in their split-signal patching method, which separates CV/mod/clocking from audio) would be doable...but again, buffering would be necessary, and in this case you'd be dealing with two different buffering methods: one for the CV banana jacks, the other for the 3.5mm audio lines. Messy but possible.
As for pedals, sure...you'd just use a 4I/O to drop your levels for the pedal's input, then raise them back up to synth levels when they go back to the AE.