We have some trouble with MS MSI installer (which seems to be able to work with/install only 32 bit DLLs) and wonder if PDFNet can run in Any CPU mode instead of 32-bit / 64-bit.
Could PDFNet.dll be provided as ANY CPU, rather than 32-bit and 64-bit
but you could use GAC, side-by-side assemblies or copy/install the right assembly based on the architecture (for more info please see https://groups.google.com/d/topic/pdfnet-sdk/s2tSvtfoKRg/discussion).
If MS MSI installer does allow you to do what you need, did you consider replacing it with an different installer (e.g. nullsoft installer, InstalShiled, … etc.)?