Most of the time there aren't that many custom molds (they are expensive!). There are generally only a few ways caps get made. Most expensive is "Double Shot", two separate colors of plastic is used, first the legend is molded in one color (kinda built on a grid of plastic) then it's placed in the full keycap mold and the "background" plastic is shot into the mold filling all the empty space. The legends on these keycaps obviously cannot fade or wear off. Other methods include "pad printing", the legends are painted on (with a coat of sealent) (if you look at your caps and kinda see a shimmer around your legends, it's probably pad printed). Pad printed legends can be worn off over time. Finally dye-sublimation, a printing method that penetrates the plastic a few nanometers. These legends generally don't wear off ( The popular Apple Extended II keyboard is dyesubbed, I have one that I used for several years on a quadra then converted for use with usb and the legends are still sharp, though the plastic has yellowed ), however dyesub can only create legends that are darker than the keycap plastic.

The companies that make keycaps have molds for the profiles they make. GMK has the original Cherry molds (medium height caps with cylindrical indentions, Signature Plastics has a few profiles including Retro looking SA (Tall caps with spherical indentations, each row a different sculpt that gives it a gentle dish when looked at from the side), DSA (flat profile, each row the same with a spherical indentation), DSS (A medium profile generally dished with spherical indentation, DCS (a medium profile with cylindrical indentation), and G20 (a flat profile with no indentation).

So generally when you put together a custom keycap set, you pick a profile, if you want double shot legends there might be some extra molds to make, but those are pretty pricy (I think I heard about 6k a pop). If you go with dyesub you have a lot of legend freedom, but you are limited to dark legends on lighter caps.