I'm pretty sure the cyberspace levels have different default settings anyway, because I could tell I was moving a lot more slowly in those than I was in free roam. But either way, a lot of the handling settings have separate settings for free roam vs cyberspace iirc, so you can tune each to your liking (or tune them both similarly).
As far as the jump deceleration setting I was gushing about, I'd recommend at least trying that, as it said pretty clearly in the menu that it applies to both 3D and 2D gameplay (and I looked up some articles that show it working in cyberspace as well) so I don't think it'd be jarring. Matter of fact the handling is less jarring with it turned way down imo (between 0-30), as retaining momentum while jumping makes Sonic jump sorta more how I'd expect. Feels more natural. I used to fight with the jumping physics in this game, made me feel like I was hitting an invisible wall anytime I jumped, made platforming really tough on my brain, but now it feels fantastic.