The link you mentioned in your first post states:
"Incoming MIDI data (via MIDI IN or via MIDI-over-USB) is indicated by a LED on the front panel. Data at the MIDI IN port is passed through to the MIDI THRU port (not to MIDI OUT)."
It doesn't explicitly state that USB MIDI In data is not passed to the MIDI Thru, but others here have said that it does not work. I've never tried it, but I believe them.
"5-pin MIDI transfers are possible but not supported, because they are too slow."
This is what refers to Axe Edit, and possibly Fractal Bot.
I didn't understand the problem until I looked at the Sim1. I think mwd had the answer. Just use two USB outs on the Mac; one to the Axe and one to the SIM1. If you need other 5-pin devices, you'll need to use a 3rd USB port for a USB to 5-pin interface. If you lack enough USB ports, you could use a hub.