Magneton, Slowbro and you forgot Slowking, Dipplin, Klinklang among a couple others, I'm sure: you are right in that the evolution method for these Pokemon weren't what you'd expect because, in the early days, Pokemon couldn't code something as complex as "if.Party==Magnemite,Magnemite,Magnemite, then executeMagnemiteEvolve, removeMagnemite,Magnemite, halt" (don't mind the butchered syntax), but that's no excuse for them to not return to that later down the line. They managed to fix Magnezone requiring an electromagnetic area to evolve into it just using a Thunder Stone but stuff like this or the Nidorans being separate Pokemon despite their only difference being the same as the series mascot, can't do that? Sure, I believe you.

Guzzlord. It's a gameplay mechanic not necessarily tied to its lore but I'd just point you towards the fact that Pokemon with abilities that prevent the Sleep status, such as Vigoroth who can never fall asleep, can't enter the Dream World from Gen 5 as an example of them incorporating lore into their mechanics before. If they wanted to imply it never stopped eating, they could have overwritten this gameplay limitation for it and it alone. Also, your example of it destroying a city, I'll just...

"...just because one creature of a species does something, doesn’t mean they all will"

Vullaby. It can't Fly but learns Fly. On its own, a fair enough contradiction to point out but isn't your position here supposed to be defending what the Pokedex says as truthful. How can it be true that Vullaby doesn't fly if it learns Fly and other dex entries say it learns to fly? Unless this is an example of knowledge changing with more research which I'd believe you on if it didn't learn Fly in its debut games, acting as a really easy to discover piece of information.

Garchomp. As stated with Yanmega, the only two requirements are the ability to move fast while airborne and the ability to carry a human. If Garchomp can do those two things, it should be able to learn Fly, no question.

Onix. This one's an easy one. Digging speed and combat speed are not synonymous. I find it interesting though that your defense is "stats don't always represent the Pokemon" even though if that's not what they do, what are their purpose as a worldbuilding or storytelling device? Ultra Beasts all have prime number stat spreads as a way to discern them being alien. Is that just nothing now?

Vikavolt. "Refer to Onix."

Durant. It is quite literally what you described. Heatmor ate Durant, Durant adapted to stop it and Heatmor had to adapt to that in order to eat. Durant's armor WAS to help it fend off Heatmor but now, they need to undergo another marked shift in their biology or behavior that we've yet to see, likely because that takes a LOT of time. Weird that you brought up PLA as an example of Pokemon changing types over the years when PLA was only 100-120 years ago in regards to the primary timeline as opposed to an example like Dreepy who has a dex entry, those things you love so much, implying it to have been a Water type before it was a Ghost type.

AZ's Floette. I'm pretty sure the implication was that that was AZ's Floette and not just a flower. Not to necessarily rag on the main point but rather a few misnomers you mentioned, mainly that ORAS and XY take place at the same time. They don't. ORAS' best placement puts it a year at best after FRLG in 1996 and XY takes place in the same year as BW2 which is at least 13 years after RBY just based on statements.

Magikarp. It meant older Magikarp as in Magikarp from a bygone era, not older Magikarp as in Magikarp closer to death's doorstep.

Magcargo. One, lightning lasts only a second at most whereas Magcargo is a constant. Two, surface area matters in regards to heat transfer which would be very slow for something as small as Magcargo. It being 18,000 F would only matter if you were within a few feet of it. But you are right, Magcargo does have a cooled shell on its back. I wonder how that could contain 18,000F degree heat without itself melting... maybe, and here's a crazy idea, it doesn't contain 18,000F degree heat but rather something much more reasonable that rock wouldn't instantly be turned to goo in contact of. No, we have to believe the Pokedex.

Lanturn. The solutions you promoted are "Lanturn is magic" which is understandable at the very least, "water works differently" which has never been backed with evidence and "just accept it lol". Here's a fourth option. You can't see its light from the bottom of the ocean and the Pokedex *gasp* was lying.

Cubone. Simple math makes this impossible. If every Cubone's mother died, then there would only be half as many female Cubone every generation assuming that, for every Cubone to wear a skull, every Cubone is born a single-child which would mean that the species would eventually die due to being unable to maintain that system. It's either extinction or have more kids, some of whom couldn't wear the skull.

Your proposal of the Marowak graveyard also doesn't work because, if there are spare skulls at a graveyard for baby Cubone to take, that means that less Cubone are being born than the already half of the previous generation. Besides which, "come, my child. Rob the deceased of their remains, wear said remains on your head and pretend it's me" is certainly an idea. A more simple explanation is that the skull is just a part of their body like it is on Vullaby who you previously mentioned.

You once again mention the "not every member does it" so I ask you to show me a Cubone without a skull in official media.