Good question....answer = it depends! Quality fit and finish on many high end production knives, is easily equal to most middle and lower end custom folders I've seen. The difference is in the ability work with the maker to personalize the knife the way you want it, with different handle materials, blade materials, shapes, specifications, decorations, etc... I think if a high end production knife fits your needs, and has options that satisfy you wants, (for example, to my way of thinking the Microtech LCC D/A, and Sebenza come pretty close to my vision of what an EDC folder should be), then you should buy these. I bought and frequently carry both of those I've mentioned above. When ordering one of these, you don't have to wonder what you'll wind up with, and most have worked out significant deficiencies, and refined their design in advance, through repetition, until the end product is about as close to a commonly accepted vision of "excellent", as a knife can get.
If you want art, or something different or unique, as I want a slightly smaller folder, with conservative clip or spear point blade, but with extensive and well executed file work and stag handles, perhaps even engraving. Then custom is the way to go! It's important to choose a knifemaker who's tastes match your own. Commissioning a custom knife, is a real leap of faith. After all, even if you can interact with the maker directly, they are starting with a pretty much blank palette, and have only their perception, of what you say you want, to direct them. It's their vision, and their experience, not yours, driving their creative process, and exerting complete control over every stage of production. You can't, and even if you could, shouldn't, try to exert this kind of control. All you can do is pray the hundreds of small decisions he will make while creating your knife, will result in a knife that will suit your tastes. For example, Striders and Terzuola's are excellent knives, and highly prized by their owners, but many of the one's I've seen just don't suit my tastes, W.D.Pease's or D.Heathcoat's work or even a small Carson #4 Clip point would come much closer to satisfying my personal tastes.