Why does the following message appear during the password setting in FineReader?
The message is just a warning for the users to be aware of the fact that password protection applied for a PDF document cannot 100% guarantee that the specific actions restricted by the user won’t be possible in some other applications. If a PDF itself is not password-protected and only some operations are, then the PDF itself is not encrypted, and it’s quite easy to bypass such restrictions.
There are applications that may not undergo or support Adobe/PDF standard policies of restricting specific actions. Therefore, in such products, it may be possible, for example, to print a PDF even if printing was prohibited by the author of the document in FineReader.
It shouldn’t apply to protecting the whole PDF from opening though. As in this case, the PDF content is encrypted in its entirety which cannot be disregarded – still, there are some weaknesses in how encryption is implemented in a PDF format.