This is a mobile module we're talking about. I have two; one built each way. The one with the 'loose' buildings is a PITA. I have to carry extra boxes with the structures in it and handle the structures a whole lot more, which tends to lead to damage. The one with attached buildings I just set up and run trains in minutes, and it only requires one trip to the truck.
So, how to attach? The attached module uses plastic kits that came with bases. I just cut them down as much as possible and then hid them under the scenery after gluing, then glued the structures to their bases. You can't even tell they have a plastic, kit base if done with any care.
The ones that don't come with bases, what I would do is add some strips of some material across the 'floor' of the building attached to the walls. The more 'grid' you have the more firmly you can attach the structure to the module. Then glue, or if you want them removable for repairs, screw up from the underside into the grid (this could be tricky unless you leave the roof off until this point).
For transport you may find it a good idea to cover the more delicate buildings with a simple cardboard box that just sits over them. It will help protect bumping fragile details like antennas, rain gutters, etc.