Hello, Hussein Hassan,
Thank you for the explanation. I would like to add this thought to yours.
in B1: his colleagues had a thought that he was on holiday after his holidays had finished.
While
in B2: The colleagues had that thought, simultaneously while he was absent.
Is that right?
Here I have found a new example which has the same situation:
C. Everybody thought he did not take the prize for political reasons.
He was thought not to have taken the prize for political reasons.
the explanation: after "not taking" the price they "thought", here we emphasise that the two actions didn't happen at the same but one after the other. Even though both actions were in the past.
But, in this case, I don't think that it works to write it in the infinitive:
C1. He was thought not to take the prize for political reasons.
Do you think so?