Well, you can't breathe in the Outzone as it is not terraformed, if that helps your theories out any. Sure would be kinda fun running around in a pressure suit constantly. Doesn't sound good for logistics.
Of course Omni-Tek has enough satellites to pick up any large scale surface base. Hell, Kennedy set up the blockade on Cuba from spy satellite photes in 1962. I hope you agree we can be assured they have no surface facilities. Unless of course Omni-Tek has been instructed to 'ignore' certain anomolties on their surface scans.
This leaves you under the dirt somewhere. Once again, unless the above caveat holds true, they couldn't be in the Outzone undetected. Any underground facility would either emit a ton of thermal energy as compared to the base planet temperature or simply expose itself by the outgassing of O2, CO2, and other by-products of an underground camp.
Rubi'Ka's native atmosphere is not breathable if the narrative of the first two prospecting teams is to be taken at face value.
Underwater could be a very good and unexpected place to hide. The water would act as a nice heat sink and refuse distribution medium. Probably impossible to detect from space.
But, just the fact that we saw Drake tied into Omni-Tek headquarters and were described his underground facility leads me to stand firm in my belief that the Dusters are in something similar provided by the same people who provided for the housing of Omni-Tek's shadow and de'facto CEO.