I don't think your thrusters make any difference on what temperature you get in supercruise. At least I've never noticed any.
Temperature depends on power consumption. Thrusters consume power in SuperCruise so they contribute to heat generation
Clean Drives consume more power than Drag Drives and will generate more heat in SuperCruise, but they will be better while doing maneuvers on planets.
So just to confirm what you mean, If I had 2 pips in engines and 4 in systems then turned off my PD, my shields would still recharge as if they had 4 pips in them? If so then that's pretty awesome, I just assumed when the PD was off everything would act as if it had 0 pips. I've been learning a lot here the last couple days. This is what happens when I make assumptions and don't actually test things to see how they work...
Yes, everything acts like the PD is on (recharge included) but you cannot adjust pips anymore if the PD is off
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