If someone who's played DOS2 plays what comes after FoV without having played FoV, they will be "confused" regardless, and DOS1 was very well-received despite us not knowing what happened in the thousands of years between it and dragon commander. As for plotholes, I believe there is no major one if we assume ridding the world of source is the canon ending. Still, there is large prequel potential e.g. the events of 611 AD, so we'll see if larian decides that the ending of FoV is the end of the series, decides to postpone continuing the story or makes another prequel, which nobody would be complaining about.
