I do appreciate that the Lemmy Doctor Who communities are less prone to wild fan speculation and continuity semantics rabbit holes, I really do. Sometimes, though, I dip back onto the main subreddits, and boy, do they get into massive circle jerks over little things that only jar others slightly.
Having exposed myself to the fandom mind virus, but refusing to join the fray on Reddit, I'll just infodump my own head canon explanations to (apparently controversial) occurrences in the latest season of the show here:
Is the Shalka Doctor now unredacted from continuity?
In the episode "Rogue", holograms of the Doctor's past selves loop around 15 like an old iTunes cover gallery. One of them is clearly Richard E Grant, who played the a ninth Doctor in "Scream of the Shalka". The animated series was short-lived and written out of the show's canon when the 2005 revival show introduced Eccleston as the "authoritative" ninth Doctor.
IRL explanation: Russell T Davies thought it would be fun to throw in Grant's face in the line-up. There's probably not more to it.
My in-universe explanation: The eighth Doctor actually regenerated into the Shalka Doctor, but because the Time War happened and rewrote timelines several times over, 8's eventually solidified upon the events of "Night of the Doctor", where he instead regenerates into the War Doctor.
However, time being relative, the Shalka Doctor is still extant if only as a wisp of an individual timeline, because a) he is a time traveler and therefore a complex temporal event not easily erased, and b) the Time War left the time stream in such a disarray that he may exist in a state of flux (no, not that one), and either continues adventuring as an offshoot of the Doctor's timeline, or is suspended in some kind of quantum field just slightly removed from it.
Pretty handwavy, yes, but all of Who continuity sort of requires you to gesture wildly like the eleventh Doctor having a thought, just for it to make some sort of sense.
The Doctor "was a dad", but 15 "hasn't had children yet"?!
In "The legend of Ruby Sunday", the fifteenth Doctor talks about his granddaughter Susan, who traveled with the first Doctor in the early years of the show. He then pivots to saying that he hasn't had children yet.
This is despite several if not all NuWho Doctors having referred in some form to having been a dad — including 15, just a few episodes earlier, in "Boom"! So which is it?
IRL explanation: As above, Russell T Davies likes to throw in non sequitur comments and details that mess with people's understanding of the show's lore. On a positivist note, it keeps that lore dynamic and throws some mysteries out for himself or subsequent writers to glom onto, like the Morbius Doctors or "half human on my mother's side" of the past. If it doesn't stick, ignore it.
My in-universe explanation: Ignoring the extended universe here, we don't know a lot about the Doctor's life previous to "An unearthly child", and nearly none about their family relations. What we do know is that they are a very prolific time traveler, and as witnessed from 11 and 12's relationship with River Song, things tend to get complicated, and invariably nonlinear.
With that in mind, it's perfectly feasible that 15 or a future incarnation has a child (the birds and bees part, or possibly looms?) that, for whatever reason, they leave for their previous, Hartnell self to raise (be a father to). Heck, given the above Shalka Doctor explanation, he could be the father, and 15 would be off the hook. Exactly what can we assume about a Time Lord's sense of self when alternative timelines come into play?
Along with the Doctor's realization that they are an "adopted" Timeless Child, as well as Ruby's search for her bio-mum in the past season, this explanation plays nicely into the twin notions of parenthood as giving life to a child versus raising it. Add to this that the Doctor's relationship to his companions (post-Susan) have always been stories of found and/or extended family.
It all makes sense when you (don't) think (too hard) about it!
So there you have it, the Doctor Who Reddit post to end all Doctor Who Reddit posts, deliberately not posted to Reddit. The important TL;DR is, time is in flux, several things can be true at the same time, and don't break your mind thinking about a TV show.
Anything else that needs explaining?
[Edited to get rid of the quotation formatting]