I just posted about this last month, after I did a quick search of the forums and couldn't find any posts about this topic.
My feeling is the method used by thunderspy server is basically a hack of the costume system. That's why I love the Homecomming team. My impression is the Homecomming team are professional developers who build on CoH with proper planning and sound design. Modding a game with one hack on top of the next is the quickest way to break a game and the fastest route to the death of it.
I AM NOT SAYING THUNDERSPY ARE AMATEURS OR HACKS. They do what works for them and more power to them.
The Homecomming team probably has their hands full with their next plans for the game. Hopefully down the road MM pet customization will be added in a way that makes sense. My advice is to be patient.
I'd rather not have MM pet costumes at all than some hack of the existing costume system.