It started similarly for me on the potter fanfic rewrite. I’d have them starkers in the explicit, clothed in the clean, fade to black, etc. Sometimes it’d be easier to exclude a scene entirely from the clean too, like Ginny sneakily pleasuring herself to a naked Harry in the Burrow in the first chapter (because the story’s Harry/Muggle not Ginny, and Ginny’s a tad jealous with a sense of entitlement). During Harry’s summer holiday trip across Europe with muggle, Ron, & Hermione; the explicit showed them starkers practically the whole time, after Harry & Ron make sure the girls’ prank backfires to that.
However, the biggest contributor to the differences is a particular first year OC – Ash. I’d created him with problems as a foil to Harry assisting Oliver Wood in teaching the first year’s flying lesson (Wood replaced Madam Hooch), thus Harry spent the entire lesson focusing on helping Ash, to Wood’s ire, including having Ash ride on the broom with Harry. In the explicit, I wanted to make it super-awkward for Harry, so I loosened his Quidditch Robes, and when Ash grabbed around Harry to hold the broom handle between Harry’s legs, Ash accidentally holds Harry’s stiffy instead. After that, Ash simply became fun to write, as a shy character that required genitalia contact in order to trust enough to talk, have confidence, function normally with another person. This invoked a strong little/big brother type of relationship between Harry & Ash (non-sexual). Thus, the related antics basically gets Ash banished to the explicit version only… him going permanently nudist in protest of the frame-up job being done against Harry. Ash’s a “happy little accident”
I did praise my way because it’s resulted in the two versions that feel organic in writing – though I do worry a bit that there may be a sense of “missing something” in the clean, given how much I’ve been writing on the explicit side only (it’s around a 3:1 ratio on words).