The MPR should still be exactly the same, other than the config specification.
By the way, if there are any files where "R" would normally indicate "Reversed" then there could be an "X" or "Y" to indicate an open config (as you know already). If there are any files where the byte 1 (not character R) indicates Reversed, then the equivalent bytes for X and Y are 2 and 3.
I don't know, yet, about adding and removing objects, though it's on my list to consider it. If I do that function, I think it would only remove objects that have been added, not original objects that are in the default track.