This is by design. Changing the tolerance of a Rhino model to something other than what the geometry was created in produces a lot of strange behavior. Surfaces that were curved can become planar, volumes that were open can become closed, and a whole manner of other properties about the geometry become mis-matched with the processing of that geometry.
Suffice it to say that, if you are going to change your Model tolerance, you should probably recreate the geometry in that new tolerance if you want it to be valid. Changing the units is fine and you’ll be able to recompute the canvas as you normally would in that case. But trying to take “the tolerance shortcut” with bad geometry usually doesn’t end well in my expereince.
Another suggestion if your rooms are just extruded floor plates, you can use Dragonfly to build your honeybee energy model instead of Honeybee. All building geometry consists of extruded floor plates in dragonfly and so it tends to be a lot easier to clean your input geometry. See the rooms_to_stories_to_building.gh sample file that’s included in the Food4Rhino download of the LBT plugin for an example.