So if I am understanding this correctly (and do please correct me if I am wrong here), are you saying that due to Red Gyara existing, it mitigates the issues that Cyndaquil has as Red Gyara is forced upon the player (only if Gyaradoes was caught)?
If this is indeed the case, each Pokemon is tested on its own individual merits in this list. Other Pokemon that help it are, in fact, a detriment to its ranking as it was no longer an individual effort. This could be said the same with items but those have a limit more or less placed on them via common sense (Once you hit 3 Items, it becomes very unlikely that the MU in question is labeled "good")
The separation from items/HMs/TMs/leveling from catching/receiving other pokemon is a false dichotomy. All represent various forms of mitigation.
HMs are the least impactful mitigating factor (to the extent of being almost trivial unless a sequence break is required for their effective use, and thankfully in GSC that isn't the case) because the plot demands their acceptance by the player, and use on one pokemon does not generally represent an opportunity cost to the same pokemon or another (the closest thing to a detriment would be using flash/cut on a pokemon that is movepool rich before getting to the deleter, but that is not really a serious thing on almost any practical case, and represents a misplay by the trainer anyways)
We have talked to death over the years the TM opportunity cost situation and how much it matters. But for example: Abra is good if and only if you buy/use punch tms. Those tms are not expensive, not out of the way, (low opportunity cost) but without them abra is just meh. Likewise leveling and availability.
When it comes to using other pokemon the metric is quite the same. How much does it cost the player in effort/opportunity to obtain, is additional investment needed etc? In effect, every single pokemon other than the starter is partially impacted by this metric already. Abra not being available for the first two gyms is a detriment, but unless one picks chikorita and doesn't grab anything else to help along the way, the common argument is already that that part of the game is sufficiently easy/trivial that it can still be S tier despite missing out on what is 4 major battles (if you exclude sprout, slowpoke well, and think it will contribute to whitney). *Which for the record, I am 100% okay with. I am not trying to say Abra isn't S-tier, just using it as an example*
Recognizing then that a static pokemon that is forcefully encountered as part of the plot of the game would be the next closest thing to an automatic addition, that is a relatively low opportunity cost in and of itself. Then the question becomes how much investment may be involved in using that resource (pokemon in this case). Well in the hypothetical of the weak spot for Quilava in particular, the parts of Jasmine and Chuck that it struggles with (note that is technically only two major battles with the leveling rules we have laid out),
the static Gyarados requires *literally 0 investment* (though HMs make it work faster). No leveling, no TMs, nothing. I cannot emphasize enough that dynamic as to why this makes the particular situation different from most other 'partner pokemon'. One only needs to catch it and go. The major penalty is that it does indeed represent a sequence break to do. Not a challenging one, but opportunity cost indeed, and we semi-arbitrarily state that these major battles are harder than the ones that others miss out on, so we assign a larger penalty to the pokemon for missing out on them.
---
To circle around to your comment, this would be true of any pokemon that has a singular problem period in the run that is mitigated by static-plot required pokemon. Of course, when you look at others near the top of the list, it just so happens that very few of them gain anything from the Gyarados. Spearow/Kenya is slightly aided in Crystal by the availability of Suicune, but Gyarados/Spearow/Suicune/Totodile struggle with mostly the same pokemon (when applicable), so they don't really gain the same way that cyndaquil does, as well as offering much more general overlap in offensive coverage with each other.
Abra doesn't gain offensively, but there are some very specific threats that it quite enjoys having either static around for their bulk.
I haven't used Magmar much, but thinking about it, Steelix is annoying though the 20-40 window is Magmar's most disproportionately powerful phase in general (so likely not much help).
I'm not sure if geodude gains much from Gyarados existing... [I am fully willing to look into all of the mons here]
----
The base assumption is a team of 4 anyways. It is not as if this bends the rules or changes anything whatsoever.
EDIT: tidied up some verbiage