In my opinion, you should always use the prime tower, although I could be wrong. This is because not every layer has enough substance to balance it out. However, you can make the Prime Tower significantly smaller.
Now, to answer your question: It depends on whether you print the entire support in support filament, which very few people do because it’s expensive. Or you print the support in PLA and only the intermediate layer, i.e., the contact surface, in support filament.
How exactly the slicer does this is beyond my knowledge if you completely dispense the Prime Tower. As I said, all the options are more about keeping the Prime Tower as small as possible. I’ve seen printouts that skip the prime tower, and most of them didn’t look good anyway.
But to sum it up briefly: Yes, you’re right, you shouldn’t mix different filaments.
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What makes more sense, the better alternative: a flush object, but only if you use the same material. You place as many of the objects as possible on the plate that need to look good, and one object that doesn’t matter, e.g., a functional part. Then all the excess filament is injected into it.
On the left are the objects that need to look nice, on the right are functional parts where the color doesn’t matter. From: Ukdavewood
