Agreed TSR tried to link everything together under the Planescape banner, heck they even dropped a little piece of Cerillia into Ravenloft, but why is that a bad thing? The point has been made this detracts from the "BR-ness" of the setting, but the fact it exists in published material makes it de facto part of the setting.

The revised MotP still allows for movement between different Prime Material Planes (interestingly if I remember it right the method it uses is via the Plane of Shadow!). The cosmology of a particular world is just that world's view on the multiverse. The multiverse is not actually aligned in a Great Wheel (or in that Tree-thing they use in FR) so whatever view of the cosmos is appropriate to Aebrynis is only appropriate to Aebrynis!

All I'm saying is leave the hooks there.

WotC left enough hooks in MotP (Sigil etc) to keep the Planescape fans happy and also left the door open for moving between worlds, why not do the same for Birthtright 3E? The fact that the continuity is already established is a bonus.