I believe the Mini's remotes can be programmed to individual boxes, but more importantly they still need line of sight to the box. You'd need to run an IR extender from each TV's location to their Mini, as well as the A/V cables, and coax or cat6.
Or, alternatively, getting Tivo RF remotes (Slide Pro) would eliminate the line of sight need, but I couldn't guarantee the signal would reach.
If running all those cables is a bit much, it'd be easier to hide the Minis with the TVs. Does either TV have coax running to them? Not sure which Roamio you have, but you could create a moca network and the coax would be all the Mini's need run to them in the bed and bath.
Setting up a MoCA Network for Tivo