I think SMS is considered a part of the military, not apart.
You can recall that Alto is given an option of joining the military or quarantined due to witnessing the alien first hand. It seems that by just joining SMS, its considered as military at least in Cathy's eyes.
So SMS must at least have some government sponsorship and influence. In addition it must also have a third party sponsorship that we do not know who is it yet that grants a mercenary group access to incredible resources like YF-25 planes that is supposedly to be still under testing, Reaction weapons, a Koenig Monster and a powerful Macross ship that despite being only a 1/4 size of a macross class, outclassed the two capital ships in this episode.
That's hell of a funding and I doubt a normal mercenary group could even access such resources.
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