A normal PDF exported from a document editor parses fine and gets rejected by nothing. The PDF that causes trouble is the scanned or image-based kind, where the text is a picture and the parser finds an empty page. The test is selectability, not the file extension.
Try it yourself: open your PDF and drag your cursor across the text. If you can select and copy the words, a parser can extract them. If you cannot, your resume is a photograph of a resume, and the extracted record shows up close to blank.
When an application portal states a preferred format, follow it and move on. Otherwise, a text-based PDF preserves your layout everywhere and parses cleanly, which keeps the human side of the pipeline, the search and the scan, working on your actual words.
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