1. Welcome to the forum and, if you're new to MC, welcome again.
2. The issue that you bring up has been discussed one or two times that I know of, mostly in the context of trying to preserve settings when reinstalling the software. Unless you save the registry settings, they go away.
3. Your own experience with 2 library modes is another important example of why jriver ought to think about this, IMO. I myself, batch converting my WAV library to lossless FLAC, inadvertently converted a few albums to 128 kbps WMA after a reinstall. So I agree it's agravating.
4. IMO again, MC is the most powerful media organizer on the planet, and indispensible when dealing with large libraries like yours. BTW, there are many users here whose huge libraries may provoke envy (sorry). My lossless library is close to half a terabyte, but that's tiny compared to some of the folks who post here. 100,00-track libraries are not unheard of, and there is at least one maniac that I know of who has over 300,000 tracks. Even if most of it is just bird calls or kazoo bands, that's still a lot of tracks.