You've got a point there.
I think interception should happen in interstellar space, negating the need to model relativistic object behaviour in star system. You'd need some special equipment to locate one and lock your nav system to it (or maybe a mission to trigger the lock). FSD takes care of the rest - not less plausible than the possibility to hover a few (thousand) km 'above' a black hole and to leave at will.
The problem with that though is if we were able to somehow drop out at the generation ship (which I'd probably venture guessing is something the Elite Federation of Pilots maybe with the help of UCC locks us out from) we'd stop in deep space with no relative point like a stellar object or station and witness something along the lines of a capital ship coming by.... but at .6C and be gone out of sight quite quickly. But that also brings yet another point... right now we are confined to the dot on the map we hyperspace to (and have our entire frame of reference set). If these ships are steady flying, they have crossed out of a solar system's space and may well be between two dots on the map. This is something FE2 and FFE could get away with but not ED in how "space" is structured, unless of course we are wanting to rekindle the whole idea of introducing "dark systems" which are not on the map and I'm perfectly fine with that!