This post was very timely. The very day it was posted, I had a plumber in my basement working on a toilet. We returned from being away for a week to a smelly basement bathroom. I had a lot of projects to do and decided to call the professional. He diagnosed that it seemed to be a wax ring on the toilet and his iPad showed a flat rate of $350. Ouch. But I knew that I did not have to do the work and while the wax ring may be a cheap part, there was a possibility of a bigger problem (which he warned me about). After removing the toilet, he found the flange was cracked and the previous owner had gooped a bunch of caulk around it. Out came the iPad again, new flat rate - $850. Again, ouch. But it was a flat rate for the job. Turned out that it was a rough project that took the professional over 3 hours to do (I knew he was having problems when I saw the Sawzall come out). I checked on him a couple of times (offer drinks, cooling fan, etc...) and saw the great work and parts that looked higher quality than what I would have bought at the big box store. It was worth the big bucks and I did not have to do the work.
I know that I could have stopped the project after the diagnostics and paid the diagnostic fee and fixed it myself and saved some money but for me that day, I valued my time and I valued the quality of his work too much. Different projects mean different decisions. The OP had the time, tools, and talent for that project and he paid for diagnostics. For me, that day, I did not have the time (and my talent was not up to the professional) so I gladly (ok, willingly may be the better term) wrote the check.