To me hand made means just that a hand made knife where there could be 1 or 20 of the same knife, some good example of hand made knives are the Anzas and the Grecos you used to get for $60, even the Dozier Arkansas Toothpicks at $225 hand made with loads of identical knives made great example of hand made.
Custom to me means you ordered the knife with specific requirements, ie specific blade steels, specific hardness, even to the point of collaborating on materials, design and function.
It,s the difference between a .22 Ruger Mk 2 and a .22 Thomson Center Contender, (maybe thats a bad comparison but ya get my drift).