Any reason this is not enabled by default? Is there a way that's considered better to store artwork/albumart?
As a guess, I'd say it's because Windows Media Player automatically saves its crappy little album thumbnails with the name "Folder.jpg", and doesn't always play well with other kids. In theory, someone could spend a lifetime saving high-quality artwork in MusicBee then accidentally launch WMP and lose it all. It's unlikely, sure, but why risk it when MusicBee can use any name you choose?
What's "better" really comes down to personal preference and how you use your music.
Most devices and mobile apps I've seen have different naming expectations when looking for artwork, but will work if the art is embedded in the file itself. On the other hand, if an album has 20 tracks, and you have a nice high-res 1MB cover image, is it worth an extra 20MB of disk space to embed that in each file? You could make a separate low-res version to embed, but is that worth the extra hassle?

Bee excellent to each other...