It's certainly possible that Apple has intentions other than to make the platform better and a discussion can be had on if the tradeoffs are worth it, but it's ridiculous to claim that there are zero benefits to anyone but Apple.
We're talking about what Apple could be planning that would violate the GPLv3. As long as the signing can be disabled by the user, there shouldn't be a GPLv3 violation.
I also expect zillions of helpful nieces/nephews would flip that checkbox for their uncles/aunts, and, accidentally or on purpose, leave it that way.
Even if that isn’t true, making it harder for malware to flip that flag already is a rational reason to implement it this way.
I do worry very much about SIP becoming impossible to disable some day. Don't ban knives because people might cut themselves.
1) Gatekeeper makes it harder to run malware; unsigned executables don't run by default, and signed malware can have its developer keys revoked by Apple.
2) SIP makes it harder for malware to modify system files.
The obvious "rational" business benefit to Apple is that:
3) Gatekeeper makes it harder to sell Mac apps without Apple getting a 30% cut
I know it sounds crazy, but they have for years now been taking steps - like this - which nobody seems to find a rational cause for, but which step by step seem to remove obstacles of technically, legal, or user expectations in line with making OS X an app store only platform, and if possible completely replace OS X with iOS.