If you're using Auto-Align 2 on Stereo Channels, please follow these steps:

Click on the two arrows on the upper left part of the UI and then.
Configure plugin channels --> Input Buses --> Input --> Named channels -->  set to "Stereo".

Now your stereo tracks will remain stereo.
You can also right-click them, go to "Track Mode" and change them to Multi-mono or use Sum-to-mono.