This is the one Scherzo I've never studied, so forgive my comment here, but, to be frank, I can't detect a difference in the two versions! With this piece, as the others, I feel each bar as one beat and subdividing into 3/4 and 4/4 doesn't work for my ear.
At your current very slow tempo, which is way below tempo, is it perhaps just a psychological thing you're experiencing? I mean, getting this up to tempo means each bar is just one big beat -- 3/4 or 4/4 notwithstanding. It goes like the wind. Why would you want to feel it any other way than the way it is written (in 3/4)?
I probably don't get what you're doing here. Sorry. Don't mean to sound rude.