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Universal monster rules started with 3.5 and the OGL thereby. Paizo updated them several times. So, it's a late addition. You can tell because they still talk about the DR effect in the older demon entries, and such things aren't in the 3.5 Demon/Devil subtypes.
So, it was first in the individual entries, then Paizo updated it to the race subtypes, and then just made it a universal rule to save time.
Every copy of 3.5 Monster Manual I have read has had the language that creatures with an alignment subtype can overcome that type of DR with natural weapons and weapons they wield. I even pulled up a pdf of what says is a first printing of 3.5 Monster Manual 1 and it has that language, so again no, it is not a late edition. Unless I remembered this wrong or the PDF I am looking at is wrong then it has always been this way. I'll look for my physical copy of it(Or some kind board member has theirs around and can look it up).