I don't think the exact contents (or lack thereof) of the preys stomach maters as much, but yes, you are right, snakes have evolved slowly over a very, very, long time, and they ingest allot more than just the "meat" of an animal. And some species have definitely evolved to require certain things, based on the types of prey they are most likely to eat in the wild. Most of the common specieskept as pets do well on a diet primarily of mammals, with the babies eating mostly pinky or fuzzy mice, which are relatively high in fat, and possibly low in calcium. But a baby mouse with a belly full of mothers milk, that may be entirely different. Snakes that are more specialized bird, lizard, or fish eaters can be trickier to keep, as they may require more lizards for food, as they are generally lower in nutrition, and some can have problems if constantly feed a diet of "fatty" mammalian prey.
Point being, we really don't know what exact nutrients each species of snake truly needs from each part of a prey animal it eats, but we do know that most snakes have evolved to eat whole prey items, so most people go with that.