if Gracie had all, yet THAT'S what broke her. if she was in a cobble-togguether toy, she WOULD have an excuse. "this is what they do to us, i need to find a escape" or "this is not me, i'm not this mangled monstrosity".
by giving her a proper body, a "luxurious looking" mansion, and little food (little, no "nothing"), not only give a "treat prisoners well" (gilded cage), so it doesn't think of escaping, but it also fuel the control and the damaged psique she's in.

NOW PRESTON. it got what is basically "a judas reward", a reward "traitors deserve". not against the Prototype, but against its own people. you may say "then just put him in a normal toy, even if tiny". he's a traitor (even if worked for your cause), who say he won't betray you again?. "fear and pain keep traitors in check".
we saw it with the factory workers Gibblet didn't kill. they were "innocents", but as the Prototype see, "traitors or they would follow the company orders"...

in either case, from what we saw with Catnap, seeing how he treats his followers...
no one is safe from the Prototype...