Chimney flashing plus "hot mopping"?
TF tape is a good idea behind flashing if installed properly, but should not be considered a seal by itself. It is more of a second line of defense in case any water makes it's way past the counterflashing. Sinse your contractor is talking about "hot mops", I assume this is a flat asphalt or bitumin roof. With the good quality cold asphalt products available today, I'm surprised anyone would still hot in a small flashing job. We really need to know if this is a flat roof and/or what material was used on the roof.