You're right that APEv2 is the format for my old ReplayGain tags.
A: I'm not using the other tool anymore. I used it for a decade to add ReplayGain tags to tens of thousands of audio files, which I'd like to to use in MusicBee without re-analyzing and rewriting tags.
Also, although I don't use MP3Gain anymore, it only supports writing to APEv2.
B: Changing the format MusicBee uses to store tags is a simple change with big implications. Switching it to APEv2, and then rescanning audio files, allows MusicBee to read the old ReplayGain tags. But, then my library's tag format for primary tags will be changed from ID3 every time I modify tags, and I'm not excited about that.
Maybe this issue isn't really a "bug," since as hiccup points out, it's a matter of different metadata formats in the same file.
When I was generating these ReplayGain values using MP3Gain, that was when I was still using Winamp. Winamp was able to handle reading both the ID3 main tags and APEv2 ReplayGain tags at the same time. If possible, the same functionality in MusicBee would be ideal.