If the USBMS tool never even *ran*, then there is absolutely *no* code in KOReader that will touch the mount table[1] (and you'd have noticed if it ran, because it has to stop & restart KOReader
).
[1] With the exception of the *external* SD card, which is remounted sanely on start & exit, but, again, that's outside of KOReader, it's in the startup scripts.