First of all, "custom" or "hand-made" does not automatically equal "high quality". I've seen many people on this forum over the years present valid complaints about the poor quality of the custom knives they commissioned. Of course the good makers who cared about the satisfaction of their customers, and their own reputations, made it right. But it's somewhat mind-boggling that a custom knife maker would send out a knife with clear and unacceptable flaws (uneven grinds, bad fit and finish, etc).
One issue with going custom is that you have to deal with the personality of the maker, and his personality can change. He might be nice and friendly in the beginning when your talking about commissioning him to make you an expensive knife, but after he has your money his personality might change, and suddenly he isn't so nice and friendly.
And then there's communication. Same as above- communication can be great in the beginning, and then after awhile you can't get in touch with him, and you have no idea what's going on, how long it's going to take to finish the knife, or if it will ever be finished.
And that leads me to the risk involved. When you are dealing with a one-man operation, if anything happens to him (health problems, family problems, fire, natural disaster, death, etc, etc) you may never see the knife, or get your money back.
And then there's the wait time. And wait times can have a way of getting extended. Six months could turn into a year, then maybe two years. Again, this is the unpredictable nature of a one-man operation.
And even if the maker is a stand-up, honest, great guy with a long list of satisfied clients, sometimes stuff just happens (like the stuff I mentioned above), and you might not ever see the knife.
Over the years I've seen more people on this forum than I can remember who had unpleasant experiences with custom knife makers (like the things I described above). I believe that those experiences do not represent the norm, but they happen, and it can really suck when they do, especially if you paid big bucks in advance.