One thing I do (for better or worse): if I need to patch a system package for an extended period of time (like to use a fork), I rebuild the package with a different name and make it provide the original package. For example, one package I recently did this with is libarchive. I rebuilt it as libarchive-patched and in the RPM spec file, I specified:

    Provides: libarchive-%{version}-%{release}

The new package would be able to substitute the old one, but the only way to install it is with dnf shell. Since other things depend on libarchive, I couldn't do:

    dnf remove libarchive
    dnf install ./libarchive-patched-*.rpm

Instead, if I do:

    dnf shell
    remove libarchive
    install ./libarchive-patched-*.rpm
    run

then both the remove and install are done in the same transaction and dnf won't throw any dependency resolution errors.