that is one way to read it, would still make this show part of the Whoverse however, which is my worry.
Can't see why you'd think that - Robert Llewellyn was in one of the Red Dwarf US pilots and that sure as hell never became associated with real Red Dwarf, let alone become some canonical element of it.
yes one actor, if the show recasts Gwen, Ianto, Owen & Tosh it wont really be an issue, but if its just John Barrowman as Captain Jack with new characters and it left vague as to where in the timeline it could fit, and S4 is not made by the BBC proper, it could be seen as S4.