In Pages there does seem to be some impact from the different options, so perhaps they serve an interim and undocumented (?) purpose.
I am unable to reproduce this in my installation of Pages. Compiling to docx and opening in Pages shows the same results as Word, namely the header margin is approx half way between edge and page (aka body text) margin, even if the Header Margin setting says it should be different.
I don’t have the most current version of Pages, because I am on an older OS, so that could be running interference here.
Just to save everyone the time in trying to see if they do anything, it is indeed just a problem with the UI showing irrelevant options (and it’s not the only place where UI is shown that shouldn’t be, for DOCX).
Any differences observed are probably down to the vagaries of multiple conversion routines going from Scrivener native output to Pages native input. If you compile two .docx files with different settings, unzip them, and run a byte level scan for differences in the files you should only find differences in the core.xml file, where the file creation/modification datestamps are stored.
