I am dealing around with connecting the fillamentsensor directly to octopi because i print over it all the time.
There are several addons to do the job.
Do you already connect your sensor directly to the pi?
I had the same idea and I will drill a hole next to the printhead cable with an GPIO adapter for a cable to the pi.
It should work are you using the cable that came with the machine? Its Micro USB right?
I have raised the issue on Github, please comment
I use the Pi camera with a 1M ribbon cable.