After some hard hours of search for information and study of some of the export_fig package code I think that I found the answer myself:
export_fig generates a PDF by first generating an EPS and then converting the EPS to PDF. Somewhere in the export_fig processing pipeline it for this calls from its print2eps function the MATLAB internal print function. For the MATLAB internal print function THE MATHWORKS notes in the documentation that it does not support the PaperPosition information if EPS export is called.
At least in the print2eps function (as of May 2015) I couldn't find any workaround for this and therefore conclude that the PaperPosition information indeed becomes lost.
The export_fig function seems to perfectly export the figure as it also would appear as a figure on screen. Thus, if any special layout is wanted, the figure has to already show this on the screen.
I would be happy if someone could correct my findings to be wrong and/or could suggest me a solution taking into account the PaperPosition information.