I've never had my Mech skills set to auto and have always used them manually - I enjoy playing it that way. But even with stationary boss fights, if you get knocked-back, teleported etc. (yeah, gitgud I know) or have stop-start action where mobility is key, or where there are multiple targets then the removal of the grace period hurts here.
I have zero issues with the cd penalty, or the old stat penalty - they are sensible changes to balance the class, but the current MG mechanic is hard punishing in PvE. I can understand this implementation in competitive modes, but this feels like one where the PvE version needs to be a bit more forgiving (moreso considering the AI of the mech).