This combined with Lance (and future Champions) more actively involving themselves with the conflict makes me wonder if the Game Devs wanted this apathetic implication to the governing bodies, had a different idea that didn't come across (like Team Rocket being more covert/under-the-radar until the player stumbled into them), or they just didn't realize/have time to rewrite those implications because of the whirlwind that Gen 1 was behind the scenes (and remakes retaining it for simplicity). It's possible to make all sorts of cases because Kanto differs in quite a few ways from future Team Plots (Team Rocket being more long-term/entrenched and not having a "goal" for endgame so much as continuing to operate and profit), so it could be a conscious change in direction as plausibly as corrected miscommunication.
My assumption has always been that the major components of the gen 1 games were conceptualized, scoped, and implemented independently without a ton of concern for how they'd work together in a single cohesive adventure. Or probably more likely: just not enough time to properly rewrite everything so that it all fit together more cleanly in the end.
There are four major components of the original Pokemon games: collecting all of the Pokemon species from around the game world, training up a team to become the Pokemon League champion, thwarting the villains' plot, and uncovering the details pertaining to Mewtwo's creation. They largely don't have much influence on each other as the game plays out. The Pokemon League and Team Rocket never interfere (or conspire) with each other. While Mewtwo has a decent amount of backstory shown to the player (and I've
remarked in the past about how interesting and unique it is in comparison to later games), he's completely isolated from the other subplots; Team Rocket doesn't make any overt effort to capture and exploit him, and he is not utilized as a plot-centric boss encounter like later box legends are.
The rival's appearance in Silph Co is probably the one single element of the game that sticks out in this regard more than any other. Amidst all of the Team Rocket panic, he shows up not to help you fight Team Rocket, and not at the whims of the villains to help Team Rocket either, but... just to fight you. That's it. The encounter has been frequently memed for how hilariously inappropriate it is and what it says about Blue's character. It's so clearly something that was implemented without any concern for whether it makes sense narratively.
Even as a kid playing the game for the first time, it always struck me as kind of unusual that Team Rocket disappears a little over halfway through the game, with only a kind of half-baked last stand in the Viridian Gym later with Giovanni. The fact that the Pokemon League questline was instead used as the major mark of game progress--with the credits only rolling after becoming Champion--and that the Pokemon League and Team Rocket questlines never converged at all at any point was very odd to me for an adventure game, especially for an RPG. You'd expect "beating the bad guys" to be the driving force of narrative and conflict, after all. It feeds into theories about how things were originally scoped out. Dig through prototype notes and information and you'll find all manners of scrapped ideas pertaining to Silph Co, such as wild encounter data for Mewtwo in the early maps of the building, or the existence of the Silph Co Chief as both a boss encounter and having a "hideout" in the place that ultimately became the Safari Zone Surf TM secret house (as noted a few posts upthread). Just seems like they cycled through a whole lot of ideas for what would be the climax of the story before ultimately settling on what they did.
(It also strikes me as strange that, despite the structure and relationship of the questlines in gen 1 coming across as unplanned and cobbled together, so much of this structure was nevertheless maintained in future games. Like, it's always been really weird to me that the villainous team plots of gens 2, 3, and 4 always seem to resolve precisely at badge 7. There was a sort of novelty in the concept of Team Rocket not being the final adversary of gen 1, but the act of pigeon-holing every regional mob after them into such a similar place was just an incredibly weird and strict adherence to formula. It's also funny to me that if you choose to dawdle and take your time in DP, then it means that Sunnyshore City is stuck in a blackout for weeks on end because that's as much as they bothered to rationalize gating you out of that section of the map before dealing with Team Galactic.)
I also think one of the interesting things about SV is that it
explicitly separates the three questlines: Victory Road, Starfall Street, Path of Legends, each of which corresponds to 3 of the 4 components of RB outlined earlier. You could argue that Area Zero then takes the place that Cerulean Cave and Mewtwo did for the 4th
The Fuschia City Safari Zone is a Pokemon Laundering Scheme run by Team Rocket. It is made to launder the exotic Pokemon they poach from outside the region to aspiring competitive trainers who are aiming to gain an edge over their competitors.
...
-Team Rocket is connected to several Safari Zone Pokemon in some way independent of this theory. Giovanni himself uses Rhydon, Kangaskhan, and both Nidos, while the only NPC in the game with a Tauros is in his gym. Pinsir, Scyther, and Dratini are only ever available to the player through either the Safari Zone or the Rocket Game Corner, an establishment which is very obviously a money laundering front - both Nidos are also sold there. Lastly, it's a bit of a stretch, but Paras are only found in the wild in Mt. Moon, a location in which Team Rocket explicitly operated in the story - the ones in the Safari Zone might have been poached from Mt. Moon, the same as the Clefairy also sold at the Game Corner.
Even as a kid, it did not escape my notice that there was a ton of species overlap between the Game Corner redemption counter and the Safari Zone. It pretty clearly suggested that Team Rocket was involved with the Safari Zone. If not running it outright, then at least somehow extorting their business for their own purposes. It should also not escape notice that the Game Corner is the only place where you can obtain Porygon, a Silph Co creation. If you are to conclude that Team Rocket's ability to source Porygon stems from their relationship with Silph Co, then it's not a stretch to conclude that a similar relationship exists between them and the Safari Zone.
The fact that the Safari Zone is temporarily shuttered in gen 2, during Team Rocket's decline, also feeds into this idea, even if it's likely just an unintentional coincidence.
