Judo comes from Jujutsu. Kano turned Judo into a massive commercial product through exciting tournaments and heavy sparring (just like MMA is doing to TMA). Limiting it to a sporting aspect. Traditional Japanese JJ includes all of what you stated, including eye strikes, throat strikes, small joint manipulations (fingers, toes)...but these are unsporty and difficult or even impossible to spar at 100% in any dojo (ie. you can only pretend to eye strike someone). While you can spar and compete at 100% in Judo with rules.
Also, no one wants to pay money to watch people eye poke, bend pinky fingers, etc. Nor would athletes want to devote 5-8 hours a day training such techniques.
Maeda, a famous Judoka and bare fist brawler, brought his teachings to Brazil and taught the Gracies. It's not 100% certain, but I don't think he only taught them Judo. I think Maeda taught them what he knew about Japanese Jiu-Jitsu with Judo, which includes standup striking, throws, standing locks, ground fighting, etc. The Brazilians do have such JJJ techniques/curriculum...but they call it "Self Defense" to not detract from their universal CASH COW, being "Brazilian Jiu-Jitsu". If the Brazilians included these standup techniques in BJJ, then it's just JJJ and not as much BJJ.
The Gracies took what Maeda taught them and greatly improved the ground aspect of JJJ and turned it into a spinoff of JJJ. My BJJ sensei is from a long line of Judokas in Brazil with his father being a 10th degree. He was a badass in Judo when he was young (my sensei), until he said one day, a BJJ guy under Rickson Gracie came into his family's Judo dojo and whooped him repeatedly. Which was when he switched to BJJ under the teachings of this guy that whooped him.
Again, it's the sportiness of BJJ is what attracts many competitors & students....so that they can go all out in sparring and competition.