He may look younger, but when you see it at some point, he's somewhat the same height as YMX in BBS.
I know that this might not be related to this but, I've been researching about the Black Coat and found this:
The Black Coats were originally designed for Roxas and Riku in the secret video Another Side, Another Story... simply as a way to disguise them while they were still being designed for Kingdom Hearts II.
What I mean is that, during the time when they're creating a model of YMX in BBS FM, Nomura haven't thought of final face of YMX yet this is why, his face looks a bit disfigured in BBS FM model (which is the one we're not suppose to see).
Like the venom said, we're not suppose to see what YMX look like in BBSFM. That being said, we should not have anything to compare with KH3D YMX. Let's just say we did not see YMX face in BBSFM, how can we tell whether YMX-KH3D is younger or older? All I am saying is that, the one on KH3D might be the young xehanort's final look. He is not younger but the same model tweaked.
Ofcourse, all of these are theoretically assumed.