On the issue of the Sony Reader Library vs. Calibre converting tags to collections.
I have NEVER seen the Sony Reader Library EVER convert even a single tag to a collection of any sort - PERIOD.
BUT - YES, Calibre CAN DO THIS.
In fact, before changing my settings to disable this, Calibre often did EXACTLY the kind of annoying conversions that were mentioned. (creating lot's of silly collections from insignificant and inconsistent tags that it happened to find in a single EPUB).
You will find this issue discussed
in this thread, along with my notes on how to disable Tag->To->Collection conversions in Calibre.