Yeah, jokes aside, there's quite a difference between "
oh, we left behind 3 small/medium sized Pokemon" and "
oh, we forgot out 10+ feet tall dragons". The former is believable that the identities of the Pokemon would be forgotten as they would just be among the many other smaller/medium-ish (and by that I mean Eeveelution-sized) Pokemon which lived in/around the Tower and thus could likely have been a mammal, bird, bug, etc.. Meanwhile the latter would be kind of hard to forget in both the sense that their absence amoun the evacuated would likely be noticed by someone and their identities would be so easily forgotten.
Also, according to the animated series Generations, apparently as soon as the people saw the Beast Trio they become terrified of them and began tossing things at them (yes, it's stupid, but we're just supposed to go with it). If the Paradox Mons were their true form, that would make this reaction feel a bit stranger as the Beast Trio still looks enough like the Paradox Mons. Meanwhile with the former, not only would it probably take a while for people to realize of the three perished Pokemon, if their original identities were so forgettable I take it to meaning the Beast Trio forms are a notable divergent that no one knew they were reincarnated Pokemon.
AND, that's assuming the legend is true OR its even the origins of the Beast Trio species. As
Esserise mentioned, just because Ho-Oh reincarnated the three perished Pokemon into the Beast Trio, that doesn't mean their species didn't exist before. Like other Legendaries, the Beast Trio are seclusive and especially encountering one for even the most briefest of moments would have been a once in a 100 life times occurrence (if not more). So putting what I said in perspective:
- The Legend could simply be made-up to explain two unconnected occurrence: The Brass Tower burning and a Beast Trio showing up. While people often associated the Beast Trio with Ho-Oh, in general the Beast Trio just seems to have a connection with Johto Legends period. They've been associated with Celebi as much as Ho-Oh and let's not forget the Brass Tower was Lugia's tower. Could be that, after the tower was burned down, a nearby Beast Trio arrived to see what has happened and this was the first time many people got a really good look at the Beast Trio as they surveyed the destruction. Thus, later on, people just connected the Beast Trio to the Brass Tower burning. The few who knew the truth either never knew this done, cared to correct the people, or were brushed off.
- If the legend is true, it would be direct evidence that the Beast Trio serve as envoys to Ho-Oh and that it can at the very least reincarnate other Pokemon into them, though it doesn't mean the three perished Pokemon were the first.
Let's also not cross off that the Terastal Phenomenon allows for some interdimensional mingling. Whether you believe that the the Paradox Pokemon are from a different time or imagined into existence, that alone leaves the door wide open to being able to access parallel dimensions (an idea which has been played with before).
NEW MYSTERY:
Or rather:
NEW TIL: Apparently Dipplin isn't one Pokemon but two! Did you think that Dipplin was just an Applin which became a candy apple? Well, turns out Dipplin is actually two Applins who share the candy apple: one acts as the head and the other is the tail (which I guess means it's responsible for movement).
So, why? Why is it now two Pokemon? Is it because Dipplin can stick its head out from the top of the apple? I assumed either Applin could do that and just didn't want to or upon evolving grew long enough where it could stick its head out from the top of the apple. Flapple and Appletun are singular organisms so it's not like Applin ever needed a second wyrm to become stronger. Also, as far as I can tell, since the two Wyrms are in-sync with one another and the Core-Wyrm never shows its head, they look like just one singular Pokemon anyway. Am I missing something? Why make it two Pokemon?