the way I see "custom made" is similar to buying a suit...
You can go into M&S and buy "off the shelf" and get good quality, maybe mass produced, in trend, probably a little cheaper, only set sizes. Equivalent to just buying a bat from a shop or website and getting the standard bat mass produced bat (big brands)
You can buy an off the shelf suit and have it "tailored", have the sleeves shortened, trousers turned, etc etc. This for me would be equivalent of requesting a specific weight, grains, pick up, etc etc. But essentially an off the shelf bat with a little tweak for your needs such as weighting. (middle ground and most would offer this I guess)
Finally you can have a "bespoke" suit where the whole suit is made specifically to your own requirements. This is the equivalent to custom bats and where bat makers earn the corn. You go to a custom bat maker and hypothetically you can have what you want. Pick a cleft, have a chat about pressing, profile, weighting, I could go on but you get the idea. each batmaker similar to a tailor would have his "style" of profile, pressing, branding which is part of the appeal for me.
Of course, as with a bespoke suit a bespoke bat could still be a stinker, but hopefully with a good batmaker you'd be able to develop something unique for you, and get something you really want, and most importantly helps and compliments your game.
Just my opinion, and not sure if the suit analogy works, but for me thats why I like and appreciate the batmakers who offer this, feel free to shoot (suit) me down, ha ha! Sorry if that was a bit long too!