Yeah it really didn't make any sense how in scenario B, once Mr X appears the roof gets blocked off, but you can still go there in scenario A when that part in scenario B occurred first.
There's no reason why they can't touch up on that this time.
What they should've done originally was use the destroyed area models caused by Mr. X in scenario A, and we would've been left to assume it was William... then to see that bastard the second time round!