I've heard PDFs aren't great in automated resume filters because the OCR doesn't work as well. Is it possible that you prefer PDF because of a survivor bias (PDFs that get past the filter are better for you but fewer PDFs get past it)?
I'm in the staffing industry and deal with automatic resume parsing tools. They have no problem with text PDFs that are saved from the source.
Example of it handling a scan of a document that’s rotated ~100 degrees and physically cut in half with scissors here: https://siftrics.com/hydra.html