Success!
I discovered this reader called ReadEra. It reads both pdf and epub, and also mobi and djvu, and it's not making any copy of my files in internal storage. Has anyone used it? From what I am able to gather as an Android noob, you have to allow the reader to scan your files first and once all the books are scanned, they won't be duplicated in another location when you open them from file manager. This is exactly what I wanted - something similar to my PC experience where I can just browse to a file in explorer and read it, because navigating from within the reader does not retain the folder hierarchy.
A big thank you to everyone who took their time to help me out!
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