They say that you can upgrade the purchased disc, digital or PS4 digital bundle versions, and that you can't upgrade the PS+ version.
So if you have the disc version and also got the PS+ version, you can upgrade the disc version. In the worst case, you'd need to do it using a different user than the PS+ one, but I highly doubt it would be the case.
Yeah, that's probably the case, I'm just pointing out that's not what it says if you take that sentence literally. It says that if you have claimed the PS+ version you're not eligible for the upgrade. That's it. Not "of that specific version".