The reason is that /e/ include the old version of Pdf Viewer Plus as a (hidden) system app. It may be possible to uninstall the system version - search the forum for “Uninstall system apps” - and then install the up-to-date version from F-Droid
Indeed, if /e/ is going to include apps as system apps, even though many people have no need or use for them - they really should make a point of always including the most recent version. I was going to suggest creating an issue in gitlab, but there’s one there already:
https://gitlab.e.foundation/e/backlog/-/issues/1348
The defect has 3.3 as the ‘target’ but it hasn’t been modified since January this year. I have added a comment to the issue, but you might want to add one yourself.
Good luck