Yes you are right, synchros are probably going to be the problem here but like I said, considering we have a confirmed failure of a part that has a lot to do with how the gearbox will engage gears, it is more practical to replace the known failed part before proceeding further. I think you would agree that if he went out and rebuilt the gearbox, only to find it was a simple solution, that he would be quite upset.
It's not a matter of 'replace every problem you see in a car' but moreso assessing the condition and judging whether there are simple resolutions before embarking on an expensive gearbox rebuild.
Even if it ends up being synchros, at least when the gearbox is rebuilt, he will have a 100% correctly functioning hydraulic system. New slave cylinders are only $100. Big bore was not necessary and neither was the clutch line, but then again, no one told him to go out and buy anything either.