Well, this thread wasn't about that and that'll be endless if we're starting to debate about that I guess, so here is my last reply. ?
My only answer is: That depends on the series on MD. Example: Tonikaku Cawaii or 5Toubun. We would normally use another writing imo.
In the end, MD will sometimes take the official romaji. If instead of Dignified asleep Saeki, they wrote Saeki san ha nemutteru, I would likely use this romaji on MD and there's likely no one to complain about that.