Here's a short and simple video on how to export an ArcGIS map for use in the PDF Maps app. It was put together by the Smith College Spatial Analysis Lab. It uses a live USGS topo basemap streaming from Esri and the geospatial PDF export feature of ArcGIS. This may be a bug in ArcMap. I just tested with MAPublisher to export a map as a Web Mercator Projection (known in MAPublisher as 'WGS 84/Pseudo-Mercator' EPSG: 3857), opened it in Adobe Acrobat and the coordinates and geospatial information is available. I tried exporting a document in ArcMap 10.2 that was in 'WGS 1984 Web Mercator (auxiliary sphere)', opened it in Adobe Acrobat and there was no geospatial information. I would try and follow up with Esri tech support to see if there's more information about why it's not working. In ArcMap, you don't need to set a 32000 max resolution, that may make the file size too large to handle. You could try a higher resolution (360 or 720). Also, depending on your data, you may want to try a larger scale (perhaps 1:30000) and a larger layout. Source.