Or they kept Mark alive to study him.

Manipulating molecule to create an entire living tree is much harder than making a building properly. Plus she’s got have some kind of sense of existing molecules sos that means she could largely copy the strcture of the existing building to rebuild the rest.

Cecil is literally just doing what he was doing in Season 1. Looking into every possible weapon against Viltrumites. I’m sure he’ll have no qualms about using them against Mark if he needs to but I don’t think he’ll use them against Mark unless Mark ends up like Omni Man.