Is a non-conductive layer required between the electronic device and the interior of these bags?

Yes. The more protective layers the better. Wrap your device in cloth or paper and then place them in the EMP bag. Place this EMP bag inside another EMP bag. This process is called nesting. Then place the bags in a Faraday cage. Your devices should now be protected.

I have a small 8x11 for my phone and spare car keys. Should the phone charger be kept in the faraday bag too?

I would say yes because it has a long cord and is electronic. I have not had to use my thank God . But I have batteries. And a phone charger and even a radio in the bags

So i could just wrap everything in aluminum foil?

I imagine you could if you made sure it was totally sealed. Some things I wrap in foil and then put in a Faraday cage for extra protection. The nice thing about these bags is ease of use. It’s nice to be able to just slip a laptop into one and seal it, for example.

Why does my car key still work in one of these bags? If they are blackout shouldn't my car not recognize?

Because these bags don't work very well. When I use it with my cell phone- I put it in the smallest bag. Then I put that in a medium bag. Then I put the medium bag in a large bag. 3-4 bags and it pretty much works. With just one bag- this product does not work.