While Capaldi might be the 13th, it really doesn't make much sense to adjust the last 3 retroactively. If Voyager introduced a secret Enterprise between B and C we wouldn't suddenly start calling the D the E and the E the F, etc.
While it's not exactly the same, NX-01 does pose a very similar problem. How many instances in TOS, TNG, DS9 and VOY were there where Jon Archer, his crew and the historically important
first warp five ship should have been mentioned... but they weren't?
We might make allowances for phrases like 'Fifth starship
to bear the name' and all that, but there are so many other occasions where NX-01 should have been a topic of conversation in 24th century Trek, but it wasn't. (Nemesis excepted, of course.
The reality is: canon changes
sometimes. Star Trek canon has grown to accept NX-01 despite a lot of evidence that was (previously) contrary to its existence, and I'd like to think -- I'd like to hope
-- that Doctor Who fandom would be big enough to accept Moffat's blatant retcons at face value, and allow their perceptions of the 'canon' to be similarly evolved to accomodate that every Doctor since 2005 needs to be bumped up +1.
I'm not naive enough to believe that will actually happen, though. Fandoms can be a spectacularly finicky lot.