Yeah, there’s an open issue or two about it:
https://github.com/emberjs/data/issues/1750
Maybe you should mention your use case there… I think it’d be valuable for you to do so.
Actually, probably better to use the “mother” PR discussion: https://github.com/emberjs/data/pull/1606
Tho it seems it’ll be fixed by an upcoming version which is being called the “single source of truth” branch.
There’s also further discussion about it here: Ember Data fixture adapter saving record loses has many relationships - #6 by kurko