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Okay so, it seems like the kombat kard chest counter does NOT count the soul chests. This makes a lot more sense now. It only seems to count normal koin chests, hidden chests, flaming chests and shao kahn chests.
Going off my earlier counts though that still totals 485 (and that's not counting the 25 head chests), and I'm sitting on exactly 450 opened according to my stats so I have no idea where those 35 unaccounted chests are.