This actually makes me wonder in turn, if the HM originate from the Area Zero crater, why do we not see any Titan sized Pokemon down there? I get for gameplay purposes that they're limited to high rank raids, but theoretically shouldn't we see a couple other Titan sized Pokemon down there if the Herba grow there naturally? Is it possible the HM just don't work that way in their natural form and had to be cultivated or selectively bred to achieve what we see from the Titans (akin to how humans bred for specific strains of things like Bananas or other fruits to suit commercial sale)?
Alternate theory: maybe they are feeding on them and it's part of the concern of their escape (i.e. if a Roaring Moon gets big enough it could fly itself out on its own power)?
Huh, never thought of that.
Well, one thing we need to keep in mind is, once again, Quaking Earth, who is a Titan Paradox Pokemon. So whatever reason Pokemon outside of Area Zero is becoming Titan Pokemon, it can't just be because the Area Zero Pokemon have just adapted to eating the flora within Area Zero.
Nothing suggests the scientists who re-planted the HM did anything to them genetically, so the only factor that seems to be at play here is the environment. Maybe, since HM are a species of plant which have been irradiated with Terastal radiation, planting it someplace lacking that radiation has caused a change in its chemical or energy makeup.
If I were to hypothesize (about this completely fictional plant & scenario which has no basis in reality), could be HM outside Area Zero have a large build-up of Terastal radiation within it than ones in Area Zero. While in Area Zero, since the entire environment is irradiated by the Terastal phenomenon, the radiation is "evenly" spread out so, for Pokemon who have adapted to living in that environment, it doesn't cause them to grow or more violent (though it could explain why they're high Leveled, afterall HM have powerful medicinal uses). But outside Area Zero the environment is unable to absorb Terastal radiation as readily, so all the Terastal radiation that HM create when it grows remain inside it. Could be why it and the moss surrounding it glows while flora in Area Zero don't, there's so much Terastal radiation built-up it's causing a release of energy wherever possible (such as generating light).
So, when a Pokemon eats this non-Area Zero HM, be them a normal Pokemon or a Paradox Pokemon who escaped Area Zero, the excess Terastal Energy causes a massive power increase within them. Luckily for them, instead of a myriad of painful ways of dying, their bodies quickly adapt by just growing bigger to contain the power (though they also become more vicious).
Why does Bruno have Onix in almost all of his teams? AFAIK his FRLG and HGSS rematch teams are the only ones where he doesn't use at least 1, and in the former it's only because they both evolved. It's neither good nor Fighting type and it's not like Kanto doesn't have other fighting types for him to use.
In addition with what everyone said above, I also like to think there was a sort of "bookend" thing going on.
Onix was meant to be the first "WOW" Pokemon the player would encounter. Up till then the most amazing Pokemon the player had encountered were the Starters because of their elemental attributes. All other Pokemon up till than were mainly just animals with some not-so farfetched elemental capabilities. Facing Brock, first first Pokemon is Geodude, a strange creature which is a living rock with huge arms. Interesting, but no more fantastical as your Starters, maybe a bit less so. Than, after defeating it, Brock sends in his ace: Onix, a giant rock snake. Despite how the battle goes it looks intimidating, and if you don't have anything super-effective against it or uses Special Moves may take you a while to whittle it down. It's pretty much the first "boss" of the game.
Jump to facing Bruno, the near end of the game in midst of the final boss rush. You've now seen most of the Dex, met many more of the fantastical Pokemon there are, made a whole team of them infact. First Pokemon that Bruno sends out? Onix. The first "boss" of the game, still a giant rock snake, but now looks less intimidating. Not only that, Bruno is revealed to have TWO Onix, and none of them is his ace! He just has two Onix on his team which are nothing more than fodder now. It just goes to show how both the player and the game has progressed since you started playing it. The single Onix some players may have struggled with at the beginning of the game is now just two Pokemon you easily can swipe aside, and the game recognizes that as they are just mooks to try and soften you up before Bruno sends out his actual Fighting-types. Oh, and Bruno isn't even the final boss! There's still Lance who commands legendary Dragon Pokemon and the surprise twist that your Rival, the first trainer you battled who started on the same day as you, is the Champion (another bookend itself). You've both come far from where you started, and now you're even going to surpass that.