But he clearly has a point. The Doctor as an outsider estranged from his own people
So that means the Doctor is gay, and not bi or asexual or demi or incel or never bathes or anything else? (Those options are just as possible, but - in all cases - that's the fun of keeping it all open-ended or implied.)
and customs, often flamboyantly dressed, unmarried

, hangs around with beautiful women but often doesn't seem to notice them...
Even though, for the most part, the show - also most exemplified by JNT's era - avoided "hanky panky" because that's how shows for kids were treated at the time. Inference is based on fact but is not the fact, but correlation equating causation can also be just as variable. (JNT said the phrase, but for the sheer bulk of the run, it was an unspoken rule. Indeed, the fact "The Aztecs" has the Doctor unwittingly making cocoa to appease a local so he can get at a copy of the tomb plans her kid has, when he's told the real meaning of the cocoa preparation and he throws a spazzy face, it's pretty much clear he's
not trying to get beyond her clothing for some hankypankying. (but at the end, he keeps a broach given to him as he had an emotional bond. There's a difference... unless one's demisexual (meaning "asexual
until there is an emotional bond developed and then *boom* the libido starts up", but if that's what viewers want to believe, that's as great as any other reason.)
Also consider that Hartnell was not really flamboyantly dressed, Troughton wasn't ("space hobo" being the moniker), Pertwee was "posh", T Baker is "Bohemian" (which isn't the monopoly of a single orientation), etc. Only C Baker could be "flamboyantly" and that coat is nowhere near as gaudy as the real-life fashion that would follow a year or two later. Then again, those awful pants WERE. Six just had no dress sense. McCoy? One look at that pullover vest would have been enough for everyone to look away, but if people are playing in archetypes then his outfit is more "nerdy?" than anything else.
As for the companions, which were male-light and especially after the Troughton era ended (or early Tom Baker if you include UNIT or at least the Brigadier as a companion), those were often deemed more "for the dads" (at least as observed by viewers, if anyone on the production team said so outright then it's a different story) and it didn't matter how smart or anything else they were. Apparently, this goes back all the way to the 1960s, where some - like Innes Lloyd - said the phrase outright:
https://www.radiotimes.com/tv/sci-fi/doctor-who-guide/doctor-who-closing-time/ (Look beyond the phrase and how the character archetypes are utilized and there's often more going on that's also more interesting.)
Even setting aside facts such as the first director of the show being a gay man, or the obvious gay themes in episodes like Curse of Fenric,
Or Ace trying to seduce a soldier because it's "more adult", never mind where the 1990s New Adventure novels went and some of those felt more juvenile, ironically. As for Ace in that story, where JNT disallowed Judson and Millington being gay as well*, Ace's "more adult" moment is perhaps more likely due to being of a sexually active age and using an age-old tactic (could be many thoughts on this, each not incorrect as that's not my thing)... and soldiers were lured back in the day and long before WW2 as well. By the time "Fenric" was made, the show was being buried by competition and JNT's bosses - who would have intervened if the same thing was attempted five years earlier - clearly didn't care. But yet another example of why JNT disliked "hanky panky", the following article does say outright why:
https://randomwhoness.com/2014/01/31/the-curse-of-fenric-1989.
* Maybe there's enough being hinted at in the script, or viewers are reading into it - coupled by making-of documentary reveals from the makers. At the same time, he didn't stop the excesses of violence, smoking, etc, on screen that increased between seasons 19 through 22, and even 23 and 24 have some grizzly ideas buried under the veneer of "light and airy camp" as that dilutes it. Apart from the melting of Kane, which prompted more letters than several hundred alphabets from across the galaxy. Or several dozen, it's only known that the BBC got calls and letters over Kane's melting being too graphic (geez, look up Snyder's from "Earthshock" and her demise is far gorier... but not as corny.)
or the fact that it's always had a large gay following.
True. How many reasons there are, of course, is the next question. The show was pretty much hands-off with any overt sexuality in general and gay guys, for one example demographic, likely weren't there for gawking at the companion for 23 minutes each week.
The show can clearly be seen through a queer lens.
Perception prevailing, there are more lenses than in an optometrist's office. As written by a person called "queer" but back when that word was used as an insult against non-heterosexual people as opposed to defining "something or someone that/who 'is different compared to most'" as a generic term, for which some claim has been reclaimed, but that leads into a completely different argument that harks right back to... perception.
Note, that doesn't mean it's the only lens Who can be seen through, one of the show's amazing strengths, and reasons for its longevity, is down to the fact that it can tell different kinds of stories, this is a show that can appeal to a wide range of people
^^this
Also, if it needs to be mentioned, I'm "B". Kinsey figured out some differences in the 1950s if nobody else prior had and, since then, the graph has been superseded by a more complex and encompassing table as well...