The motor doesn't generate much heat or noise, but I do stick on the pannier the sole of an old thong (flip-flops - I don't know what you call them in the US) which is about 10mm thick. I put it there not to protect the pannier but to protect the plastic case of the motor on that side. Although thinking about it, it would insulate as well.
Now a bit of philosophy. When we took up touring the outback our first choice of transport, as I said in my original post, was horseback. But we're not horsey people so that wasn't possible. We'd been bushwalking for years and thought of travelling on foot, but you can't do that in the outback because of problems with carrying enough water. So bicycle it was.
We wanted a 'human-scale' experience that was slow and where you experienced the environment around you - the dust, sweat, sound of birds; where you were locked in to your situation by the mode of transport; meaning, if you were hungry or it started to rain and you wanted to get to the next town you couldn't just press the accelerator a bit more and travel 100km in the next hour. A bicycle (or horseback or on foot) forces a bit more responsibility on you as you have to be self sufficient. I designed the add-ons for our bikes just with that in mind - five days of self-sufficiency. For instance, I built the rear panniers out of 1/4" steel rod. If I ended up with a broken frame on some lonely outback road 200 km from the nearest town, and maybe not a car passing for the next two or three days, I wanted to be able to sit on the back of Jenny's bike so she could double dink me.
We wanted to go touring. The mode of transport was largely irrelevant, whereas most people in these forums have chosen to go touring by bicycle and leg power. Our mode of travel is just as human scale as a normal bike: we can't go any further in a day (in fact, usually a lot less), we can't get there any faster; we simply have the option, if we want, of assistance up those hills and against those head winds.
But yes, it is different. We don't have the sense of achievment that a pedalling cyclist has. We simply wanted to travel at a human pace and we've done that.
I'll finish with a Rodney Rude style "Don't you just hate that!" motor-assisted bicycle joke:
Ya goin up hill so you put the motor on. But there's a strong tail wind and it blows the fumes all over you. Don't you just hate that! Or, you're goin downhill, pretty flat really, and the headwind's so strong that you have to put the motor on. God I hate that!
It's not all beer and skittles with a motor.