My Kinda Guy
On a more serious note, it depends on the heatsink design of the amplifier and how things are laid out. For example a JL has heatsinks on one side, designed to be mounted ass down, mounted ass up the transistors still face the same direction and convection currents are STILL HINDERED although upside down MAY BE BETTER in that instance.
Some amps have the heatsinks on either side with fins that run horizontal, ideally (although the amp makers don't tell you this) you want them mounted on their END because the air will flow over the entire heatsink area with little to no turbulence as if they were mounted "properly" I'm sure we have all seen competition cars mounted this way and never wondered why.
Until we know the whole story we cannot pass judgment.
As for utilizing the thermal protection, bad idea, it's there for PROTECTION not as a feature, if you are consistently thermalling out your amp you have an install issue or did not bring enough beer to the party.
Chad
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