Another case of different players referring to certain musical things differently. I agree with your point about one chord may suddenly jump up to a different inversion and sound funny even if it is the correct chord. Sometimes regenerating that track may fix that or changing the chord slightly like make it a basic D instead of a D7 may do it. I'm an organist and I will change inversions or even octaves all the time but of course I'm reacting to the song itself and using my ears. The organist who did the RT's doesn't have that luxury plus when Biab chops up the RT to match your chords you can get all kinds of things that a real player probably would not do at that point in the tune. All we can do is work with what we have, nothing's perfect.
The comment about using Real Band is good if you're trying to produce a finished product because in RB you can edit sections of an audio track like that organ part. Somewhere in the tune that chord is probably playing the inversion you want and you can do a copy/paste to replace the chord in the exact place you don't like it.

Bob

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