It's not only iBooks. Instruments does too. You can apparently re-sign Instruments just fine. iBooks deals with purchased content/DRM and probably has some extra protections baked in, or it relies on the code signature being Apple's for accessing some protected content. I've never re-signed that app so I couldn't say.
The reason you aren't seeing it elsewhere is most things aren't code signed with the library validation option. The Core Animation issue is 100% reproducible even in super simple applications if you code sign them with that option.
To be clear: Nvidia can't fix this. It's an advanced security feature of macOS and it is working as designed. The problem is the security is hostile to third party video drivers, probably because taking that into account was not part of the design. They simply don't officially exist; all other video drivers are provided by apple.