Im only speaking from a BMW AUC warranty POV.
In the last 6 Weeks my car has had the turbo actuators changed, brake sensors replaced, rattling exhaust valve fixed, oxygen sensors replaced and engine management light fixed. Each time it has been in i have removed the JB4 and haven't had any issues with warranty claims.
It could be that; They haven't bothered to check to see if it has been remapped, they can't tell or they don't really care. Either way all problems have been sorted FOC.
On my last visit i spoke to the service manager about the fact that i will be getting Coilovers and ARB's. He said that the car will still be warrantied excluding all suspension components, which is fair enough as they are no longer BMW items.
Also, last year, a friend of mine had his V8 lump replaced FOC by BMW 1 month out of warranty. He had an evolve remap and akropovic exhaust system which was removed before the car went in.....
Like JamJay says, i think that if the engine needed replacing they would probably investigate further. But what they can really find out i'm not sure???