Honestly - I've never been bothered by any apparent inconsistencies in Doctor Who, although I know a lot of people are. I'm more troubled by things that don't make sense in Star Trek. DW is more fantasy in that it can always explain things using Time Travel and alternative dimensions - Time And Relative Dimension In Space (TARDIS). Star Trek on the other hand is more Science-based storylines, and that is great until it does something stupid.
Speaking as a hardcore Whovian, lately, the continuity issues (especially the UNIT dating issue) don't really bother me that much. Really, the dating of the UNIT stories comes from dialogue in Pyramids of Mars clashing with what happens in Mawdryn Undead, and honestly, I'd rather ignore Sarah Jane Smith claiming she comes from 1980 in the former. The novelisation, at least, makes it vague.
Honestly, there aren't many problems in franchises like this that can't be waved away with the MST3K Mantra. Just saying.
IMO, only the TV show and most of the BF audios are indisputably canon, albeit with maybe a few of the New Adventures thrown in for good measure.
Now that's technically BS. It only happened twice.
The first time we see Atlantis is in The Underwater Menace, which is set in the 70s. Those were the ruins of Atlantis society, in caves deep beneath an island. They get flooded again at the end, but that has nothing to do with the original destruction.
The next time Atlantis is brought up is in The Daemons, where Azal, when telling the Master not to fail him, says, "Remember Atlantis!", implying that the Daemons had a hand in its destruction, but only implying.
The last time Atlantis appears is a year later in The Time Monster, with its destruction in ancient times actually shown to be caused by Kronos the Chronovore, albeit unleashed by the Master's machinations.
The spin-off novels, while of dubious canonicity, claim that the Daemons were the ones to give Atlantis the crystal that held Kronos' power. I think this was in The Quantum Archangel.