Actually this post has kind of lodged itself in my brain this morning, and I've been thinking more about Steve Urkel as a character and a prototype or template for this trope, and the total stranglehold this character had on American popular culture for a fair while in the early 1990's.
(I am old enough to have been alive and more or less aware during this period, and watched a good bit of "Family Matters" during its initial airing, yes I am that old, sorry if that's a shocking revelation to any of my followers)
For a bit of background - in the 90's pretty much everyone was watching the same 5 broadcast network TV channels and popular culture was a bit more homogenized that it is now in the era of streaming where everything feels more niche. Trust me when I say that basically everyone knew who this character was at least in passing.
ABC had a very popular block of sitcoms it aired on Friday nights called "TGIF" and "Family Matters" was part of this programming, along with stuff like "Full House" and "Step by Step" and later "Boy Meets World" and so forth. They rotated in and out, some of them were pretty short-lived, you can look it all up on wikipedia if you are so inclined, but some of them ran end on end for years and went well into triple-digit episode counts.
"Family Matters" was one of the breakout success shows that ran for multiple seasons, and Steve Urkel was a big part of it. The character was meant to be a one-off gag in a season 1 episode where the daughter character of the main family was to be embarrassed by going on a bad date with an extremely unpopular classmate who was obsessed with her.
(Frankly given that "nerd" stereotypes up to that point had been pretty much uniformly white, I suspect that a Black actor was cast primarily because the producers wanted to avoid the controversy of an interracial relationship and for no other purpose. 80's and 90's sitcoms were very racially segregated as far as main casts went.)
But crucially this character epitomized everything in OP's post linked above - the garishly colored tops, the bowtie, the suspenders, the highwater pants and unfashionable shoes, the whole rigamarole suddenly appeared in full on basically every TV screen in America with Steve Urkel. And Steve Urkel ended up instantly and extremely popular.
It does really beg the question of why mainstream (majority white) American culture ended up grabbing hold of this character with both hands and running 10 miles with it and you could probably write a dissertation on it. There was a period of time around 1991 or so where Urkel was just fucking everywhere - suddenly there was a cereal brand and other tie-in promotional items, the "Urkel Dance" that was a thing for a hot minute (and you could buy the accompanying song on a cassette tape, naturally), and ultimately the character ended up in crossover episodes on basically the entire damned TGIF lineup, including episodes of "Full House" and "Step by Step" and so forth.
The key thing here is that the character was not introduced with the intent of being likable. He was portrayed initially as a pest to the main cast and particularly to the daughter in the Winslow family that the show was centered around. He was his own pastiche of stereotypes about clumsy, socially inept, clueless, asthmatic intellectuals.
I don't think he was ever intended to subvert any racial stereotypes, either, per se, he was meant to be a cartoonish clown at first, and while in later seasons he was made out to be a kind of underdog character, that definitely isn't the portrayal that initially endeared him to the (mostly white) audience.
Anyway I don't know that I have a specific point here and none of this remotely invalidates anything OP is saying, except to add that I don't think this "nerd" stereotype was first put forth as an attempt to subvert anything. Maybe it became that later, but my knowledge of popular culture kinda fizzles out around 2010-2015ish as I don't watch a lot of tv or movies anymore, but I think it's worth noting where this came from in the first place