I have been advised to report this to the synctex maintainer from the MikTeX bug list:
http://sourceforge.net/tracker/?func=detail&aid=3465114&group_id=10783&atid=110783
Issuing in MikTeX:
xelatex --interaction=nonstopmode --shell-escape --aux-directory=./auxdir --synctex=1 file.tex
produces X, Y offsets equal to 0 within the synctex file, so the code is misaligned with the generated pdf.
On the contrary:
xelatex --interaction=nonstopmode --shell-escape --aux-directory=./auxdir -no-pdf --synctex=1 file.tex
produces the correct offset information in the synctex file.
Therefore, running both in sequence produces correct results overall, but requires 2 compile runs.