Size itself doesn't really matter. A ton of character's sizes are inconsistent, even in regards to characters of the same series. Besides, the only thing that matters (EDIT: when basing a character model off of another character model) is that the skeletons match up. You can otherwise scale them up without any issues, so if Black Shadow needed to be taller, they could do that. In fact, doing so would make him look a bit beefier as well.
Isabelle is a bit different, as she's not only taller, but much thinner as well so her arms are in a completely different location from the Villager's arms. This isn't really the case with Black Shadow. Also, the Male Wii Fit Trainer is a bit bulkier than the female Wii Fit Trainer. It's not by much because the hitboxes need to be the same, but it does show there is a bit of leniency in that regard, even moreso for Black Shadow because his hitboxes are allowed to be different as an Echo Fighter.