I've researched the subject and have found almost all info needed to construct a batch command pipeline except how to get all keys from .reg file (or from command line) to get properly inserted into mounted subkey.
I did found info about method involving running reg/regedit under desired user account, but i doubt it would work for user accounts inside wim and i also need to target key "HKU/.DEFAULT". I didn't test this.
I have succeeded importing a hand-crafted .reg file into mounted subkey, but this would require me to manually alter all keys in .reg file so they get under required locations.
If there is no other solution, i will try to put something together to partially automate this task.