Even if plugin delay is correctly compensated for, you can still have phase shift due to things as simple as EQ, or a cab simulator or whatever. This is potentially an issue anytime you do parallel processing.
 
If you put Channel Tools after the plugin, you can make small timing adjustments instead of just flipping polarity.

I have purchased MAutoAlign and this crazy thing can accurately determine how many feet apart my microphones were, over and over. Now I'm not sure it always makes it sound better to have it line up the signals, but it's super cool imho that it can figure it out.

You could take advantage of using a DAW. Record the output of the "amp" to a 2nd track. You can now blend, timeshift, & change polarity as needed. No real need to keep it a live realtime process.