I probably would set both builds to link to the CRT in the same way. It feels somehow cleaner. It's only that I can't really give a good reason why it should be done. You mention keeping the dependencies the same, but are they really, and is that even desirable? It's not clear what that accomplishes. The main implications of the setting seem to only really affect distribution.
The other side is, is there a particularly compelling reason to set the CRT link option differently for different builds? I haven't encountered such a situation.
Anyway, just food for thought. I'm actually still puzzling about this myself.