Murata's version returned to One's original story, 'though. They simply added a tournament filler arc, which was pretty good overall (especially how they handled the 'big bad' ?).
Not to mention, the story board of the "filler" has been drawn by One himself. He still decides how the plot goes in the new version. Murata is only in charge of the improved art, and the flow of the battles (but never their end result, that's up to One). He sometimes streams when working on the upgraded version of One-Punch Man.
Although sometimes I do think the reactions of the characters and the like seem to be funnier in this version, if you can get over the average art style.
But seeing how long it has been since One last updated his original, I'd wager he's planning on making the collab the only one and full version of the manga. He does get paid for that one after all, while this webcomic is completely free. Can't survive on free work, now can he.