Not sure how to do it with a logical editor, but your first question is basically a good feature request. We’ve had this discussion before here on the forum and I would personally like a couple of options:
Either as you say drop markers or something for where there’s a mismatch. It seems intuitive that it should be possible to do without too much fuss, but then again I’m not a programmer so what do I really know?
Force the merge anyway and just throw up a warning that there were problems. At least this way we have the option of working with a sub-par edit and address on the fly basically.
As for workarounds - other than what was mentioned I’ve gotten fairly good over the years at just looking at two adjacent tracks and seeing where they aren’t symmetrical. 99% of the time I can spot inconsistencies and address them before I merge. It’s typically either clips that ended up going even-odd tracks instead of the other way around like all other clips, mismatched fades, or ‘stray’ mono files like nat or fx that ended up on one of two channels by mistake. It sucks having to go through that but as Fredo says if they give you a ‘poor’ AAF then it is what it is. If it takes me another 5 minutes for a 42min show (USA) then that’s something I can deal with. If it takes me far longer then I likely have bigger problems with the AAF anyway and are dealing with an inexperienced, indifferent or poorly paid editor.