No, MB can't (to the best of my knowledge) be asked to differentiate between the duplicates based on a criteria - I don't know what the criteria are for it choosing. Steven may be able to elaborate.
I guess the way I would go about this would be to populate Original Album for all tracks with the original release it was on. Then, you could just set an additional rule for Original Album = Album and the singles would be picked automatically over the album tracks. You could even fudge it by only defining Original Album for tracks that were on a different release to the one they are tagged with currently, then create a virtual tag to define Original Album (Virtual) as something like (not using the syntax because I can't be bothered right now) : If Original Album has a value use that, else use Album.
In general, for more complex things involving the specifics of different releases, tags are the way to go with MB. The inbuilt functions like duplicate removal are good basic steps but aren't designed to be used for complicated criteria (and this is complicated in tagging terms, as simple as it may seem).
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