While it is true that a ‘system’ can only only be bonded once what defines a system is a bit complicated.
A generator can be bonded, it mainly depends on if it is a ‘Separately Derived System’.
If the transfer switch only disconnects the phase/load side it is a ‘singular system’. If the transfer switch also disconnects the ‘Neutral’ it is a ‘Separately Derived System’.
In some instances a a generator can be bonded, in some instances a bonding jumper (to main bonding point) can be used, in some a generator must have it’s own ground (rod).
It’s quite tricky as there are a few variables that come into play, which I wont speculate on or get into. Disclaimer: Consult with a licensed electrician or inspector.
I can’t find anything specifically regarding how mixed generator/utility service or off grid generator service would effect detection, I did find that Sense can be used with an entirely off grid application such as solar or wind.