You're printing in-house two-sided on a desktop printer, right? The misalignment you see is on spread that consist of one side on one piece of paper and tthe other side on a different sheet of paper after the printing and assembly is finished, is that correct also?
If so, there's not much you can do about it other than adjust your design, which is not a good solution it the job is ultimately destined for commercial printing. Desktop printers typically have front-to-back and sheet-to-sheet registration tolerances on the order of plus-or-minus 1/16 inch which means the total drift vertically or horizontally can be as much as 1/8 inch between successive sides or succesive sheets, and it won't necessarily be consistent from sheet to sheet. For desktop output I tend to use larger margins to disguise the drift, and I usually don't us automatic duplexing (but some machines are better than others, so it depends on the equipment), and feed from whichever tray, including the bypass tray if available, seems to give the best registration results.
Your first paragraph is entirely correct. Plus, I was using duplexing.
So, if it's really all in the printer, exporting to PDF and then printing won't make a difference, I imagine. So it looks like my best option for now is to print all the odd pages, then the even pages on the back sides of the same pages, and see how that goes (testing first, of course).
I could make a duplicate document and try adjusting the design, but there's no way to ensure the page numbers and top of page headers from the Master will line up nicely without endless experimentation.