The building takes it's own MC but it is not a 2MC. If it survives it will not be rubbled, if it fails one level, top to bottom will get rubbles for every pip over its morale level it failed by. Falling Rubble, etc, could still happen. The squad failing it's 2MC with a negative modifier helping it for the TEM, has its negative effect on the squad, CR and negative effects on any SW/Fins it possessed and since a building can't be a shellhole, it would also have a flame placed in that level.
One of the most dangerous places to be in a Bombardment in ASL is a ground level only building. If Wooden, it rubbles on a 9+, Stone a 10+ and you don't ever get to the 2MC for the Infantry occupants because they are gone.