I'm strongly considering leaving multiple pets below the max for a different reason than the reason the op listed.
For example, if I train a giant beetle and stop at 4 instead of 5, then I can ride the beetle to where ever I want to go. When I reach a hunting area, for example, I can dismount the beetle and jump on an ethy while I hunt with the beetle.
For me I just don't like traveling on foot, so ill probably stop at 4 most of the time. Its the same reason I never really hunted with a greater dragon before the publish. And yes, I know I could fly if I was a Garg, but I just don't want to be a garg.
Based on my calculations and estimated builds, It looks to me like I can have some pretty darn good pets at lvl 4 if I plan correctly, but I'm also not to far along with pet training and I'm already accustom to using pets that aren't up to the GD level.