I agree that the lore has to be considered a lot when designing the game and creating encounter tables, but I think we differ on what has to get priority when the game is created. "Yungoos/Gumshoos are everywhere because lore says they are invasive species" makes sense on its own, but if implementing that lore leads to bad game design and is detrimental to the playing experience, then one has written a bad piece of lore. Besides, lore can easily be changed if done at an early enough point in the process. Yungoos/Gumshoos had not been established in the franchise before Sun and Moon, so nothing would be ruined by making them less common in those games - the lore could have been changed to reflect that.
It would perhaps attract some more ire if these Pokémon were nowhere to be found in a later Alola game, since Sun/Moon established that they are very common, but in Sun and Moon one could have given these Pokémon RS-Chimecho levels of rarity and changed the lore accordingly, and nobody would have noticed anything. Or at least removed them from Poni Island entirely, just adding a bit of NPC dialogue saying that the ranger corps keeps them away from the island, or that the native species on Poni are so powerful that Gumshoos can't get a foothold, or that strong currents and winds makes it very hard for species to emigrate between the different islands. Point is, it is an easy issue to address without lore getting in the way, especially so when the lore is introduced at the same time as the game is designed.
Besides, I'd argue that making the early-game Pokémon so overwhelmingly common is objectively bad game design, and that lore at best is a patch trying to fix the players' perception of the problem, rather than an attempt to address it. "Yes, these Pokémon are ultra-common, but... uhh... Oh, look at their Pokédex entries! They are invasive! There, now it makes perfect sense! It's not because we are lazy, we swear! We had perfectly good reasons for doing it this way, and there was nothing we could have done to change it for the better!"
As Taistelu said, the encounter tables is an experience-breakingly bad problem with a very easy fix. Editing Pokémon encounter tables is a non-issue when it comes to resource use in the design process. Unless the code is amazingly poorly organized, they would literally have had to change single numbers in a text file. If the Yungoos/Pikipek/Wingull problem had been addressed at any stage in the design process, it could have been fixed by one intern in half a day. I can't imagine a serious developer or game director objecting to this fix because of what the lore says. "Sure, it makes players really frustrated, and it causes some Pokémon to be prohibitively hard to find, but it is justified by the Pokédex entries!".
World-building is important, sure, and the way the world is built will affect game design elements. But when the relevant parts of the world are built at the same time as the game is designed, the designers are not tied down by the lore. If an aspect of the game design doesn't work, and no existing/established lore is sharply contradicted, then new lore should be changed to suit game design. The lore framework is flexible until the game is fully finished, at which point it gets harder as fans read and accept it, and expect future continuity/consistency. An eventual third version of the Alola games will have to address an eventual absence of hyper-common Sun/Moon Pokémon, but in the original games, this could and should have been changed, with no need to explain away anything.
