I was going to post the same request! I found a workaround, its of course not as good as to have a prefs. option, like: no automatic switching layouts, but...
As soon as i duplicated (mouse right click) my BFD3 plugin track, both, Atom and Atom SQ switch to keyboard layout! Funny!
This works with AD 2 too. Just tested it. In the Map Window of AD 2 you can switch to "GM" layout, to have the Toms on the keys 4 to 9.