It's actually a good theory... Santa has the fireball gun... Chaco looks different than other Mimigas, and wears lipstick... They are strangely isolated... and they join the researchers to get off the island. And yes, they appear at the cutscene where Sue and Itoh are being changed back to humans! (Well attempting to...)
That said... I don't think there is any hinted dialogue to that effect.
She comments about how you look like Arthur... which results in Chaco and all the caged mimigas <3 ing you...
Chaco and Santa seem pretty established with each their own residence. Rather than jump to conclusions that they are actually humans in Mimiga form, it seems more likely that Grasstown/Bushlands used to be a human/mimiga settlement. After all you have MALCO, the teleporter/computer storeroom Kazuma is trapped in, etc... Weapons like the Fireball Santa has or the Bubbler that Mimiga Village has, were probably brought there by humans. And the lipstick, maybe it was leftover, or learnt from humans...
Maybe they needed Chaco and Santa to help with the transformation; having live Mimiga might be needed for data, and they offered to help? Or maybe they just wanted to go on a vacation. Living alone all that time, maybe they saw the opportunity to leave the island, and they wanted to take it. After all they were living alone... maybe for a reason? [WANTED : CHACO and SANTA - ARMED AND EXTREMELY DANGEROUS MIMIGAS, DO NOT APPROACH, CONTACT YOUR LOCAL VILLAGE LEADER IF YOU HAVE INFORMATION]
Lastly I have an old unfounded theory that all Mimiga on the island are probably originally human. That they were the people of Ballos' old kingdom, and that either Jenka or Misery cursed them all; turning them into Mimigas... And over time it became permanent. We at least know that you can be turned into a Mimiga by Misery with Sue and Itoh. Don't know what other forms magic can turn someone into...
It seems hard to turn Sue and Itoh back/break the curse... I used to think the curse would return as long as the curser lives/does not retract the curse.