Just wanted to update and say the PS3 controller and Bluetooth associated issues were figured out.
Note: that when using the ControlBlocks and the drivers that go with it, automatically controller one and two are taken by this add-on regardless if you have actual, physical controller plugged in via USB or otherwise. A neat little trick to to save some money and not need to buy more add-ons is simply this; I disabled the ControlBlocks feature. Yeah, I will not be using the SNES and DB9 (Atari) connectors for anything legacy, unless it comes up...more than not it's all going to be USB or Bluetooth like many controllers are nowadays. So with those drivers uninstalled and/or disabled, I still needed the power switch and LED indicator to work, but would just installing the PowerBlock driver work as a separate entity from the ControlBlocks?
I went through the process of installing the PowerBlock driver, even though I didn't have the separate add-on board for my Pi, but would it work regardless for what I had inside? To my amazement, the power switch functionality worked all on inside own, and there was no interference on the ControlBlocks assigning phantom controllers. With everything looks good as I wanted it, I paired my PS3 controller and sure enough it was assigned to the first LED position instead of third. What I noticed was in Retroarch, when I hit select + X for the retroarch menu to come up, in-game, and within the emulator running, either FBA or MAME, it always showed controller one and two ready, because of the ControlBlocks, but when it got to the third controller, everything was "N/A" and not even considered by the system. When the ControlBlocks driver was uninstalled, everything worked fine against the auto-configuration. All FBA and MAME emulated games didn't discriminate whatsoever with whatever controller I was using, just like I want it to be.