Hello
today we manage that case (Engineering BOM and Manufcaturing BOM views) in the same product container, and 2 different subfolders ...
Not sure that is more complicated than use a separate Library.
Anyway. in 10.0 the move function, as you say, move the 2 views of the WTPart.
But there's a workaroud. use "cut/paste" in folders. It will move only the view that you cut/paste ... But not sure that OOTB you will be able to cut/paste between a Product and a Library ...
In 10.1 M040 , I saw in the release notes that there's a enhancement of the "move" function. We will be able to choose if we move all versions (ie all views) or a particular version of the WTPart
regards
Gregory