I wasn't one of your mechanic's eyewitnesses, so I can't say for sure if either his technique or his prognosis is correct. Actually, neither do I know if you method of checking the valve clearance gave you accurate results.
The Yamaha FZ1 service manual instructs you to check the clearances on cylinder No.1 with the piston for that cylinder at TDC on the combustion stroke. You then turn the crank 180 degrees to check the clearance for cylinder No.2, another 180 degrees for No.4 and finally another 180 for cylinder No.3 (The 4th cylinder before the 3rd is no mistake).
That's an excellent method, obviously, or the factory wouldn't prescribe it. But occasionally, especially with an engine that has quite a few kilometers on it, 40,000 km in a year is a lot, you can get a marginally different reading if the cam lobes are rotated very slightly from those prescribed positions. Ideally, valve clearance should be measured between the tappet bucket and the very heel of the cam lobe, which is 180 degrees opposite the highest point of the lobe.
But because an engine's cam timings is not split symmetrically on both sides of TDC, the heel is not quite directly adjacent to the bucket at TDC. So if you check the clearance at that spot, then turn the cams and check it again between the heel and the tappet, the clearance may be very slightly different. Usually that difference is only a thousandth of an centimeter or less, which is too small to worry about, although it can make a feeler gauge noticeably harder to pull through.
Personally: I believe your mechanic is probably right. But if you still have doubts, you could always check the clearances again using the mechanic's method...