I have never seen it done in that way and the tech places I've experience with did not do it in that manner neither - so we won't be doing it like that unless some really good reasons to do so pop up.
It shouldn't be an issue in the first place, because applying the patch in that case is just redundant and as such won't change or break anything. It just happened to do so now for a very small amount of people because of a small accidental change on our side. It's not a big deal
Edit: Although "X version to X version patch" style naming would be useful if it turns out to be a bigger issue. But I don't think it will