It's actually the layering/compositing features of the PDF spec that allow us to stamp the files; if the file is not a PDF, then the stamper app won't work. The stamper also has no way to unzip files, and even if it did, that would create a fulfillment-timing problem, since each file has to get stamped on-the-fly for each buyer only after payment is completed, and that already takes longer than we'd prefer just selling single PDFs, and especially for large or complex PDFs.
Additional stalling tactics to cover the extra delay required to unzip and rezip a collection of files (not to mention the additional time to stamp more than just one PDF) would only defer buyers' gratification even further, making for an unsatisfactory buyer experience. Moreover, what if not all the files in the .zip are PDFs? What if they have different authoring passwords? What if, what if... It opens a huge can of worms that reintroduces the very problem we'd introduced stamping to avoid, namely, the unsatisfactory buyer experience of DRM-style approaches.
Have you considered simply recompiling each of your PDF file collections into a single PDF for each bundle?