The problem often enough isn't whether something can be implemented. Rather, it's how much time developers can dedicate to their hobbies...
That said, it would certainly be possible to restrict the display to a certain file type. But I'm not sure if I really understand your problem. I mean, you're the one putting a mix of files in one and the same folder on your Kindle and then having problems to tell them apart? Why don't you just create folders for what you deem worth separating?
MaxStirner: There were some irks with the latest versions since a rework of word recognition. I thought they were fixed? Not sure, though. I will need to have a look. If you have an account at Github, better report the problem there. I guess this is it:
https://github.com/koreader/koreader/issues/352 - not yet fixed since chrox couldn't reproduce, unfortunately