A quick note on scaling, not that I have messed with it a lot yet. Remember there is a setspritesize command as well, so you can actually use the pixel sizes rather than a percentage.
I've yet to play with the physics, but have had an idea to try since before AppGameKit was released. So I will be using it,(or trying to) soon enough.
Scaling the whole screen I have not tried, however as long as you don't scale it too much, AppGameKit does a good job of keeping image quality up. In my shooter project I scaled up the first end boss 2x and it still looked good. I was expecting it to look quite pixelated.
I would imagine the best way for you to go is to make your main level as large as it needs to be, say 4 screens long by 2 screens high for instance. Then just scale your viewport when needed, as you scroll around it. I haven't tried anything like this yet but that's how I would attempt it to begin with.