As the contents of the machines will have to be earned anyway, and given the option to just use enderio virtually unlimited energy from an expensive capacitor, I'd favor having the option to drop equipped/filled machines/tanks. Currently I'm using a 500 000 mB Thermal Foundation tank to drain 16 000 mB GC tanks …
If you feel that having to keep them in place (I'm currently at the asteroid space stations, the cargo loader might be what you're thinking of), this could be a config option and/or a per-machine option (the cargo loader would unset the flag on being drained). Machines being especially inbalanced might e.g. require you to drain their energy using batteries. So a refinery would be portable, the big energy clusters(?) would not.
I don't think this is a priority though - after having the other mods and having spent weeks on having unlimited energy. If it's easy to code and you need to relax while coding not-your current-problem, we might get lucky.
PS, tanks and machines with content/configuration should be reset-able to their defaults by placing them in the crafting grid.
PS2, I just read that it's already implemented to not drop items from the cargo loader.