Yeah, you just have to ignore this change as making no sense at all.
In the same codex it says all the rubbish about Dolmen Gates, it also mentions wormholes that they can bolt on flying transports like it was nothing, and a more versatile one that is built into every monolith. That's as well as a Necron Pirate Fleet Overlord, flying about terrorising a sector. How the hell does he do that without FTL?
More to the point, how did they fight the Old Ones without it? The Old Ones built and had complete control of the webway. This isn't even taking into account their galaxy-wide surprise attack on the C'Tan. Just give them back inertia-less drives, perhaps with a gravity flavour like the only other non-warp-travel species: Tyranids.