In my previous post I thought I had found a fix because the audio sounded good in Compressor. I was testing the audio by playing it in Compressor before starting the batch. But ultimately in the final render the audio was still reduced in quality. I did finally fix it though.
My fix involved reducing the number of nested clips. The project that was producing poor quality audio in Compressor consisted of a single compound clip and some titles and end credits. Even without the L1 Limiter the final output from Compressor sounded bad. But I noticed that the nested compound clip, when rendered in Compressor, sounded fine, even with L1 Limiters applied to the audio clips. So I copied and pasted the contents of the nested clip into a new project and added the titles and end credits there. This fixed the problem completely and the final render is identical to my original project.
All of my projects in this Library file have similar setups. I've imported the audio and video sources into my library file and then selected the clips and created a multicam clip. I then bring the multicam clip into a compound clip where I do all of my multicam camera switching. This is also where I attached 2 audio clips from different sources (room mic and sound from the mixing board) to blend them together. Then I bring that clip into my project where I can do some final edits and add titles and credits. But in the case of my work-around I have removed the last level of nesting so the final project now consists of a multicam clip with 2 audio clips attached, titles, end credits and to top it off I applied the L1 limiter to both audio clips.
My problem is solved with this workaround. If I can find a way to repeat the same issue with different data, I'll be sure to mention it.