The idea is that eventually you will be able to call LoadControlScheme() passing the name of your scheme or a reference to the scheme asset. Right now tho, as you've noticed the whole initialisation process is... kind of a mess and inefficient too.
Looking into the initialisation process and being able to swap various control schemes are big parts of my priority to-do list but I don't know when they will be done. ngl they are kind of daunting and I can't remember enough off the top of my head about how either works right now to be able to tell you what would be a good way to hack what you want (sorry!)
hopefully I'll get them done soon but for the time being sub-optimal messy rubbish is the best option (and heads-up if you do have multiple control schemes now, player custom bindings for them are probably not gonna be saved reliably)
aaaaaaah I wish this bit worked for you but it's just one of the little corners of the system that hasn't been worked on enough yet ^_^;