I hate to be the "What does that mean" guy but uh... what does that mean?
It means my guess about why your files were still peaking at -0dB or lower was correct.
Lossy files behave differently from lossless files when it comes to clipping.
If you want to learn the finer details on that it would be best to resort to professional audio websites or forums.
It's a topic you can write a book about.
The important lesson from this thread is that when you process an mp3 file that ends up with a 0dB Track Gain tag (so I am not talking about a slider position!), there still
could be clipping, and MusicBee is then correct in alerting about it.