Many of us who wrote articles for the Bell System Technical Journal would disagree. The BSTJ publishers could transform something that made sense when viewed as troff output into unintelligible gibberish. You cannot split a UNIX command line into multiple lines just because it "looks better". Sometimes format really matters.
I think that is true for any scheme -- professionals and editors need to work together. That's what Jon was suggesting. When they don't have shared vocabulary/goals - bad things can happen. FWIW: I can not speak for him directly as I never had this conversation with him (Win might have), but from what I knew/know of Brian Ried I think he might agree with what I'm suggesting. IMO, there will always be cases like the one that you described. This is not particular to any document compiler system. The question is how to bring the two sides together and who has the high order bit?
My complaint with Word and the like, is that the 'control' is hidden. It's $%^& magic -- why is it indenting here? Hey I did not tell it to make it go italics ...
Yea. There's a balance here: the number of people that tweak things because they can is quite large. and often the tweaks need to be undone because they look like @#^@^ to the professional typesetter (I guess they'd call this the publisher these days). There also needs to be some way to flag the legit "your defaults got this so wrong my readers will trip over this" bits. That's lacking in Word, for example. I've seen other systems cope with this to varying degrees of success.
I've used LaTeX for all my professional papers. With the proper style guides, I can easily transport the words from one style requirement to another. However, I run into issues all the time when I go from conference A that has a single column to conference B that has the dual columns of IEEE. Where diagrams fit and are pleasing to the eye in one, they look awkward and out of place in the other. Etc. So this ideal one can approach, but there will always be bits of bricabrack that can't be easily handled by the automation. While most of the issues can be delegated to the macros, some manual tweaking is necessary because there are many works that are more than just a big bag of words with semantic metadata attached.
I never got into troff. It always seemed lower level than LaTeX to me when I was learning things, and I didn't want to be bothered with those details. I can read and use it today, but it's not my primary choice unless I'm tweaking a work already in troff.
Warner