If we make a new ruling (sensibly, IMO) that reactive hull replaces BFI then they will only get reactive hull saves and no BFI saves.
Why would that be the case?
At the moment the Reactive Hulls-save replaces the BFI-save
where the RH-special rule applies; in any other case it simply doesn't.
So when a Necron ship is on BFI and takes damage from firepower- or strength-based weapons, Nova cannon, bombers, torpedoes, mines, asteroid fields etc. the RH-special rule applies and thus you get to roll a save of 2+. If the Necron ship is hit by a successful hit&run attack the RH-special rule does not apply, so you take the ruling from the basic rules which is a 4+-save against hit&run-attacks. If the Necron ship takes damage from a boarding action the RH-special rule does not apply, but neither does the basic BFI, so you simply get no save at all.
The clarification I posted just said that Necrons do not get to save two times against the same point of damage; it did not say that the basic BFI-rules do not apply to the Necrons under any circumstances.
RH simply improves the BFI-save under certain circumstances, at the cost of reducing the armour value of the ship on BFI. It does not replace BFI.