Well I don't believe a standard Fedora kernel package will include any modules which would trigger this taint so the question is, what other kernel modules have you installed?
Common candidates would be graphics drivers (though I think those will mostly set the "proprietary" bit) and wireless drivers.
If you can find anything in the lsmod output that you think may be a candidate then run modinfo <module-name> and see if the output includes intree: Y as any module without that will trigger the taint you are seeing.
UPDATE: The rts5139 module that you're seeing in lsmod but which doesn't seem to be on your system is probably in hethe initrd and is being loaded from there early in the boot process before the main filesystem is mounted.
That also explains why blacklisting won't work as you would have to rebuild the initrd with the updated blacklist. Rebuilding the initrd with dracut will cause the module to go away anyway though.