if you place the call to pdf24Plugin_link() in the footer then all articles of the current page will be used for the PDF file.
Inserting the call to pdf24Plugin_link() in the header will not work correctly because the pdf24Plugin_begin(); and pdf24Plugin_end(); is not called at that time. That is the reason why the call to pdf24Plugin_link() must be in the footer or at least after the pdf24Plugin_end() was called.
If the call to pdf24Plugin_link() is performed in the loop then only the current article is used for the PDF. If the call is performed outside the loop then all articles will be used for the PDF file.
The new plugin version 3.6 is more powerfull and has a mode that breaks the restrictions that the call must be performed after pdf24Plugin_end();
The call to pdf24Plugin_link() can be split into two call. You only need to call the method pdf24Plugin_form(get_the_ID()) just after pdf24Plugin_end(). This creates a hidden form identified by the ID returned by get_the_ID(). This hidden form can then be referenced from an other place, everywhere in your blog. The reference link can be created with the new method pdf24Plugin_formSubmit(get_the_ID()). This creates a link which sends the form identified by the ID returned by get_the_ID().