You all got a point, but there's one big problem: It's all speculation.
Unless a pet changed rarity at some point, there is NO saying how rare it is, therefore it would be redundant to add VRs based on the assumption that it could be rarer than a pet that's already on the list.
To get to a working basis for a rarity only list, it's easiest to just look at the pets that are on this list first. Sort them going by the proven rarity we have and then we can go from there. Discussion about which pets to add after that, I'd personally like to happen... after that. And then, if there is a pet the community wants to discuss... there wouldn't be much place for discussion. Because there would be one thing to answer for all of those: "Do you have prove that it's rarer than a pet that's on this list?" And if the answer is "no", then it would not be added.
Of course this leads to a high chance of inaccuracy, but adding all VR pets would be a bit over the top, right?
(I would still opt for at least one post somewhere at the end of the new guide to trace any VR fluctuations, because the Rarity Changes Archive isn't being updated anymore.)
Edit: Scrap that last sentence. Since the rarity changes archive hasn't been updated for more than three years, I'm going to PM Nadine about the possibility of re-doing it with only the VR+ changes.
Edit 2: A few hours later and I think I managed to get the upper half of the current list into order and caught all the fluctuations up to and down from omgsr. xD