I can only assume the behaviour is intended, and speaking for myself, it really sounds ideal.
Deleting a track from the library only (whether intentional or accidental):
it sounds good knowing MusicBee is able to preserve that old data and continue where it left off if one were to add it back.
So, at the moment, there are options for both users - one who'd want to the data back later on and the other who'd want it permanently gone from MusicBee.
The suggestion would take away the first option without affecting the other anyhow.
On the flip side, deleting a track from both the library and the computer:
It makes sense that the data is automatically deleted since the track is basically "gone forever".