Munnyspinner,
I agree, I think there was a serious problem, probably involving controllability, during which height was lost and then Nr decayed rapidly and it became a brick. At what height, I wouldn't even begin to guess, but certainly high enough that it punched through that quite substantial roof.
I don't hold with the 2 stage collapse.....I think it went straight through followed by progressive collapse of internal structures. From the pictures it appears the left side of the craft is more severely disrupted than the right, born out by the damage to the left engine from which the AAIB weren't able to prove the drive train.