I doubt there's a way to really work around it. There's probably something very different about the models of units that are mounted that makes them correctly sit in the saddle and look good doing so to boot. Even if you got them down to the right height on the mount, they would probably look really odd attacking enemies in melee - I imagine they'd still have their unmounted animations, meaning they'd be poking away at the vast spaces of air right beside them, probably well over the heads of the foot units they're trying to attack. So, it's probably best to splice in the model for some already-mounted unit and reskin it - you'll know you get a model that looks good mounted, and you can give a unit a substantially different look just with some creative skinning.