There is a way to get to where you want to go:

- Duplicate the track
- Strip silence on the duplicate
- Flip the phase on the duplicate
- Mixdown the two tracks. The audio will cancel out where there is signal, leaving you only with the room tone.

Not my best explanation - hope that makes sense.

That works to silence the audio but I want to actually cut it out the same way strip silence does. That way I can put all the sections of room tone right next to each other. That's a potential solution though if I can make it work somehow

I can see a way of building a macro to get the rest of the way.

On the track with the audio, something like:
- select next region
- set loop to region
- delete time

So I should do the first four steps in your first reply and then the second three? Or just the second three?

When I try and flip the phase using the mixtool on the second track it doesn't completely cancel out the audio I have it just makes it sound robotic am I doing something wrong? Is there another way to flip the phase?

I got the phase flip working to cancel out the audio so no need to troubleshoot that!