It costs more than it is worth to have them do better. As a framer is takes me a couple minutes more to compensate. To have the do it would take hours of labor.
I presume you're talking about scribing the bottom plate, or perhaps another board placed between the foundation and the bottom plate? Why couldn't a layer of that same sort of scribed board be placed on the foundation before placing the prefab modules?
Depends on where it was. The worst case I saw was a half wall, so we cut each stud a different length.
There are options for prefab as you saw - but when building on site we have the saws and other tools needed anyway, so it isn't a big deal to use them. With prefab they don't normally use those tools so you have to account for the cost of getting them out putting them away.