The SQLite database replaces the existing nss key3.db and cert8.db files, which are Berkeley DB files. It doesn't replace any text-based configuration mechanism a program may offer for key access.
NSS may be used to load keys from files pointed to by a config file, just as OpenSSL and GnuTLS may. It adds the _option_ of a keystore if you want to use it, but doesn't force it. The issue you ran into sounds like a heavy-handed conversion to nss done by the Fedora folks, rather than an issue inherent to NSS its self.