Wait... first the attendant said they arrived in the morning. The boss was probably at work in the morning, so how won't he know that the thugs were at the safe with his attendant?
Also, the train arrived at about 11:45pm. If the thugs arrived in the morning, it would be after midnight. How can they leave before midnight?
Either way, it doesn't make any sense.
Also, there must be intervals where the train comes and leaves.
Sleeping Pills using last for quite a few hours. It is possible for the attendant to help his friends escape while taking the pills and locking himself in the cellar.
For some reason, I think that the analog watch in the cellar is to support the attendant's alibi and testimony that the thugs came.
Also, skilled or trained people can change the setting of the watch to read a different timing.
The boss must have thought it ^ was strange and came to the conclusion that the attendant was with the thugs.