I have never in my life seen a check in agent bust out a tape measure and check all the dimensions of a bag. Suppose if it was egregious, they could do that, but for 3" they aren't going to notice/tell.

As mentioned above -- no reason VS shouldn't be tagging it for you (even with 2 tickets).

If you get it tagged by VS all the way that reduces your 1 in a million chance to 0.