There's work on creating new file manager for koreader:
https://github.com/koreader/koreader/issues/2614
Koreader also opens in certain directory (last used, maybe you also can set some default directory to be always opened, didn't played much with this) and you can set it up to open last used file. Basically, if you opened at least one book and set it to open last used book, you'll need file manager only to open new book.