UPDATE 3.21.25 *FIXED*
Seven years later (and a month before I upgraded my head unit to a new model), I found a working solution to this issue.
Too anyone who happens to have these set of circumstance happening with this model radio/head unit, with the issues I was suffering with for years (Specifically playing music from the SD card and Android Auto), here is the solution:
Have an Android phone that supports Android Auto Wireless
Get one of these, plug into the AA port (2) on the back of the Pioneer AVH-4201-NEX and this issue will *NEVER* happen aga