Audio Systems: After market car stereo, car audio manufacturers, wiring harnesses

Question
Auto technician told me today that after market car stereos in volkswagens cause electrical problems.  If any diagnositcs are to be done the stereo must be removed.  Also stated that any auto electrical shop or dealer would make you remove the car stereo before running diagnostics.  He stated this is common with VW and Audi.  Why do car audio manufacturers make wiring harnesses for after market install?  Is what he is saying true?

Answer
this may be true in very complex cars where the stereo can be integrated with navigation or on-star or something like that but I have a 2001 Jetta and the only wires in the harness were ground, constant power and the trigger from the key (and the 8 speaker wires of course) just like 99% of all cars.  The car's computer etc. has absolutely nothing to do with it, it's just power for the head unit.  I've had a few units in my Jetta and they all have worked fine.  I have also had the "check engine" light diagnosed with a code reader where the technician sat in the car, he said nothing about the CD player and was able to read the code fine as a bad temp sensor in the engine.