Some people just aren’t cut out for sales. Really, that’s what you are if you’re a one man band (like I am).
If that’s the case, he needs to have a set schedule for “as found” repairs & this isn’t merely to cover how much is required in parts, but what’s needed to comp his time as well. I can see doing a freebie & sucking up 2 or 3 sheets of decking & maybe the same amount in rafters if it’s just scabbing on some new pieces, but 20 ft. of fascia or rebuilding the area around a 6’ wide chimney that’s been 40 years without a cricket is going to take a boatload of time & that’s what needs to be comped for.
It’s possible he’s on the upside from the part of the estimate, but after that, the extras are killing him on time, parts & sub labor.
If it’s just the basic ‘strip & shingle’ jobs with limited ‘as found’ repairs needed, then he needs to do a better job in measuring the job. This will cascade into resolved issues he may have with too many or not enough parts (which means either overstock that has to be handled & maybe returned @ a % loss or having to always run to the supply house).
If his measurements are always within 5% of perfect (we all make mistakes), then it’s possible his customers smell blood & they’re always trying to get something from him. Believe it or not, a majority of customers prefer a strong relationship / strong willed sales process FROM THE CONTRACTOR vs. someone they can push around a lot.
This doesn’t mean you should bully your customers, but they are looking to YOU the contractor for guidance in a process & in materiels / how to use them right that the clients are unfamiliar with.