Alright alright I know nobody cares but I wanted to put my thoughts down so I'd be able to say "I told you so" if I'm right which i'm probably not BUT
I think the reason the gnome had so much power of the real world is because Wayne broke the 4th wall so much while talking to him. In HLVRAI Wayne makes little to no mention of the world outside the game, it's mainly coomer that acknowledges the 4th wall, and so Benrey has no effect on the world outside the game. Maybe
ALSO I think there's someone behind this. At the beginning of the first HLVRAI stream I believe he says Valve themselves sent him the "experimental copy" of Half-life but in the description for the videos it says he "discovered" it, and in the description for HLAGE Episode 1 it says that Wayne was linked a workshop page for the gnome, and goes on to say that Gabe Newell himself told people not to mod the code of the Gnome Run due to the "Myth". This is a new edit since the finale released too, and due to it's insistence on nobody else EVER playing the true Gnome Run, I don't believe whoever linked this mod to Wayne was just some random hacker.
The intelligence of the gnome is another matter. One thing that Benrey and the Gnome have in common is that, as Wayne gets nearer to the end of the game they become more and more reluctant to continue. Benrey doesn't want to hurt Gordon, or at least part of him doesn't, and the Gnome insists that they need to stop and go back repeatedly in the final act of HLAGE, but once Wayne reaches the Peppa Pig Movie (jesus christ I love all this bullshit) the gnome's tone is quite different, obviously leading to Wayne getting Gnomified. But during the Gnome's musical number he yet again sings a different tune, so to speak. I believe the combine did take his memories of his and Gordon's time together. We see him warming up to Gordon and some real character growth in the final act, but once Wayne makes his way through the vault the Gnome seems to be back to his old, derogatory way of speaking. As for the musical number i'm not quite sure, but perhaps seeing gnomified wayne and being in wayne's shoes causes him to change his mind and remember what they had together.
The person creating these mods is still a mystery, but if we connect this to the greater RTVSCU there are a few options. Tucker, the creator of the I. M. MEEN disc for example (not sure about this bit) not only shows the skills that he would need to do something like this, given Meen's AI and the ending, and he would know where Wayne lives, making him an actual threat. Wayne also breaks the 4th wall numerous times during the stream, which supports my previous theory. Of course, that doesn't answer how Wayne escaped from The Shining painting at the end, but this part of the theory is flimsy so it's fine. The most powerful AI character we've ever seen however, is Homer. The fact that this man constantly gets kidnapped by fictional characters is amazing to me. I'd have to rewatch the Simpsons stream, but I believe this metric of power could be important.
TL;DR Wayne breaking the 4th wall may have effects on the power of the self aware AI, somebody has got to be behind the Half Life AI mods, and this could extend into the entire RTVSCU as a whole