Yeah, certainly mp3 isn't the recommended format, but doesn't MonoGame provide a way to convert audio into 'binary' files or something? I don't use MonoGame and never used the pipeline in XNA, so I don't know if that's correct though.
Generally we use a lossless format like wav for asset distribution so the developers can convert that to any format they please, converting from mp3 to ogg certainly isn't a good practice since it may generate all kinds of artifacts and distortions, in fact converting from any lossy format to another isn't recommended if quality is a concern, unless of course you're compressing substantially so the quality of the source won't affect the output that much. (e.g.: if you want a very low bitrate ogg, it won't matter (much) if the source is flac or 320kbps mp3).
@EricMatyas your work is simply awesome! I don't use MonoGame but I'm here for some help with a lib I'm trying to use with FNA and came across your post. I have used your musics in a game recently (still early WIP but playable), here is the link. I didn't know you were active in this community. Just want to say thank you for your amazing contribution to the indie gamedev community!