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One of my players is a full conversion both and wants to intergrate mech and glitter boy pets onto his body, like replace his legs and what not, have any of you encountered this? And if so how’s you deal with it?

I'd halfway roll with it, with the caveat that a GB's legs have weirdly high mdc. Triax has 25 foot tall robots with brain transplants, to give a possible ceiling on size. The book Heroes of Humanity has the Hellbuster Armor for Cyborgs, and I'd go with something similarly ablative as a median between Cyborg and Power Armor. Only a few types of cyborgs can get a RPA skill, so other than having extra armor it's not necessarily exploitative. The exceptions are the Triax Luftwaffe Combat Cyborg Pilot which is stuck with a light chassis, the Mining Borg which gets one free slot by accident, Heroes Unlimited Cyborgs which have to get rebuilt, and space borgs (Megaversal Legion/Quatoria/Repo-bots/Cyberai).

If you feel like having some skill penalties for the Cyberdocs and Operators, or require any work be done at a particularly advanced facility, I'd say that's more than enough for some piecemeal bonuses.