Not real sure what the GNSS capability of a/c performance has to do with clearing (or filing) to fixes or en-route waypoints. Remember, for continental operations (not remote or oceanic) aircraft operate on RNP-2, so the GNSS component for this discussion comes to play only on arrival and approach operations.
I doubt most (if not all) Vatsim artcc's have LOA restrictions or discussions regarding en-route directs. With that in mind, I try to apply what makes sense. I do not believe in clearing someone 1000nm downrange to a long distance fix, and rarely have I seen this IRL. Clearing aircraft (on vatsim) to a known fix in the next artcc or subsequent following artcc is far enough. Additionally, a C1 should have a little knowledge of major airspace around the country and the en-route structure. In other words, if heading to the west coast, you should know there are fixes/vor where airways or arrivals begin and avoid restricted/military airspace (don't clear direct to LAX!). Same applies to the NE airspace, etc. There is a difference when the destination is MSP, ATL, MIA, JFK, SFO, vs OMA, AMA, BOI, etc.
It is an interesting discussion though...