Of course, they were in disguise!
Compass Carburettor was infamous as the latest Main Character, one that had wiped out the Luck Genre Systems on his own. So, even though he was considered dead, pretty much every System was aware of his appearance and even energy signature.
Therefore, they couldn't just saunter through with their original appearance. Hence, Stencil changed their appearance.
Originally, she planned to buy some Skills from the Astral Network to change them. But, Skills weren't absolute. Grade 2 Systems were still capable of seeing through their modified appearance.
And hence, Stencil used her own power, taking advantage of her Secret Refiner System, physically moulding their bodies. At least, the modifications of this were veiled by a mystical power to be more subtle.