Yeah, this entirely depends on the exact behaviour of the system installer. Maybe it doesn't double-check, because it assumes that SIP has never been disabled in the first place. Maybe they will add such checks later. Thats exactly what I was talking about though when I mentioned 'unpredictable behaviour'.
BTW, SIP is not preventing use of custom kernel extensions. You still have write access to
/Library/Extensions/ folder. I am not sure why Paragon kext insists to be installed to /System/Library/Extensions/, there might or might not be a good reason for that.
That's because we have to wait for Paragon to update their app. El Cap and SIP is still brand new for everyone, it is going to take several months to make changes, validate it, and then release it.
The problem that I have is Apple can't claim the system is protected if it doesn't actually do anything when you turn it back on. It should've re-ran and migrated all the existing stuff into a different location, like it does when you install El Cap for the first time.
It does nothing to protect the average user. They don't even know what it is, they just click everything that pops up. SIP will [probably] be a lot better for the average user.
UAC and SIP are two entirely separate things and Windows had SIP-type of feature for years. One has to do with authentication, the other has to do with system integrity, two unrelated areas.
Microsoft actually started to protect its system files against modifications a long time ago, so Apple certainly isn't the first to do this, they were late to this, just like everything else.
And UAC does protect users, it has gotten much better over time. Windows' security has changed a lot and for the better since Windows 7. A lot of things are not being run as admin anymore without explicit permissions from users. People write to software companies bitching about getting too many UAC, which is causing companies to adapt to reduce the need to have admin-mandated features, which actually makes it safe for everyone.
Also, Apple has UAC just as well, install anything that requires admin access and you'll get prompted for your account password. This is just as risky as it is on Windows and some malware infections were available on OS X and iOS because people were accepting these access dialogs on OS X without thinking ahead. However by default, both platforms are better in security because it prompts first rather than letting it happen without prompting the user.