Use the bookmap page sequence for maps
Set up your custom PDF plugin to use the same pages when publishing from a map as when publishing from a bookmap.
By default, pages are assigned differently when you publish a PDF from a map as opposed to a bookmap. PDFs published from maps do not use the first and last pages in the body sequence, only the left and right. But, as with almost everything in the DITA Open Toolkit, you can change that.