There are two problems I can see, one I think is minor and one I think is major.
The minor problem is, people open Apple hardware up, violate the warranty, break the product, put it back together again, and send it back to Apple; Apple has to expend resources already to prevent that from happening (in the same fashion as all consumer electronics companies have to expend effort to detect moisture damage).
The major problem is, third party companies will open up shop performing unauthorized repairs on Apple hardware. Apple can't vouch for any of that work, many of those companies may end up damaging Apple hardware and upsetting Apple users, and Apple has a clear business interest in making it less easy for random people to enter that market.