I am using Reader (version 2022.001.20169) with a M1 Macbook.
Reader adds .pdf extension to every filename despite having turned off this option in Finder (I have unchecked the "Show all filename extensions" option in Finder).
I have tried to turn on and turn off the Reader option in Preferences > Documents "Always use filename as title". This also makes no difference as the .pdf extension is added automatically when creating a new pdf file, or editing an existing one.
Edit and convert PDFs
When you enter the file name into the Save As dialog, don't add ".pdf" to it. It's added automatically. If you do add it, the file will be saved as "X.pdf.pdf", which is probably why you're seeing it in Finder, even though the extension is hidden.