I don’t play in 6mm so I have no answer for that scale. In 20mm we just put the figures inside the building. If the roofs don’t come off then the figures just line the outside walls and you tell the other players what that represents. I don’t see the flags as being any different to a counter, they are still on-table markers. How can you like one and not the other? If anything the flags are more jarring to the eye, unless that is the effect you are after.
Less enthusiasm, please. This is Britain.