A few questions
For machines to activate bunker they must control the region, correct?
There is a human control token on a region (3p game here) and a trog war party token, machines move in and attack the region. Who controls the region if troggs win control region objective?
1.) Yes you have to control the region of any structures you want to activate.
2.) The Trogs will gain control, in a 2 and 3 player game that is handled differently. That said the human control marker is NOT removed from the region until the control objective is resolved.