Big Finish's audios all work togather in one continuity, and they also incorporate RtC into their continuity. They so far haven't done any audios set after RtC, but one of the original characters from RtC has made an appearance in one of their audios.
If Lara's new books seriously contradict the audios, then I may need to rethink my stance. Already I admit it could be considered a strech to reconcile The Salem Branch with the audios, but there is a 12 or so year gap between TSB and the full cast audio stories from Big Finish. Plenty of time for untold stories to sort out the continuity issue.
Since Big Finish did an abridged audiobook of Angelique's Descent read by Lara Parker, I think they have embraced the 18th century backstory as part of their canon anyways.
I already can see one way around the issues that could come up. Liz could have lied in her will about Viki's paternity to hide a different secret, or even to give Viki what she most wanted, a family and identity. I definitely prefer Liz to be Viki's mother, because it's what the writers intended, and because of the warm chemistry between the actors/characters. Watching the show I definitely feel that Liz was her mother,and I think there's subtext to support that, but of course, subtext is personal and subjective.
This is of course just my opinion. Of course others are free to feel differently. There are some good stories in the spin off media that are well worth any fan checking out.
For what it's worth, there's also some very very good fan fiction out there. Stories can be enjoyed without being "canon", and in DS, with Parallel Time, all realities can be real somewhere.