How have the manufacturers responded to the elements that can affect paint on a typical carbon mountain bike?

You have 2 options it seems:
1 – Powder coat the frame if it is alloy. The limitations are in the colour choice and the designs limitations but it is as hard as nails.
2 – The other option is to apply many more layers of paint and lacquer to absorb the shock of chips. Usually a typical road bike will receive about 2-3 layers of lacquer. In this example, this Trek MTB has about 8 layers which is clearly an indication that they want to protect the exposed surfaces from abrasion and chip damage as much as possible. There are other brands which apply std 2 pak bike spray in this many layers. Others opt for weight saving but it depends on what the bikes primary use will be.

That said there is no particular right or wrong way to paint a MTB other than the point that std bike paint can take a hammering on loose terrain compared with road bikes and therefore the manufacturers apply different solutions to MTB spray jobs.
The best overall solution, if you want to keep your bike is good aesthetic condition, is to apply Invisiframe which is a thin clear adhesive tape cut to your bikes profile. Works a treat.