This is something mator and I had discussed as desirable, and I mentioned it to Freso and he said I should put it here as a feature request.

Basically, when LOOT decides to move mods around, you can either click "apply" (thereby accepting all its changes), or close it (thereby accepting none of its changes).

It would be nice to be able to accept some changes, but override others (without necessarily making a meta rule every time, especially as I've had issues with circular meta data in the past...)