Ok. I played around a bit, and yes, if you store a file inside the local or iCloud folders for Documents the file will open in Documents by default. I expect PDF Reader is the same, since Documents is just the big brother of PDF Expert.
Two options, you can use the Share Sheet as discussed to force a file to open in Pages, or you can store the Pages files somewhere other than in the main PDF Express folder.
The two most obvious options are to store your page files in the Pages directory (or sub directory), or to create a new folder in the Files app and store them there. You can still get to those files through PDF Expert if you want to. Just use the Files option instead of the PDF Expert option when selecting connections in the left column.
Or don't use PDF Expert to handle Pages documents at all. I'm not sure why are are doing so to begin with.
I'm also unsure why you are saving articles to Pages. It's not a very good app for archiving, read later, or research. What it is good at is creating documents, either to print or export into PDF files. I have a few workflows that use Pages and Documents (PDF Expert), but I keep the original Pages files and the PDF files separate. On the rare occasion I have a Pages file in the Documents folder, I tend to open it directly in Pages when working on it, so I've never encountered the issue you are having.