The clear container just happened to be by chance, not design.
Sure you can use a powerhead. Anything that will push or pull water would be fine as long as you can figure out how to conect it. Baffles would work well I'm sure, but I'm not interested in 100% water flowing though the media. The media I have in mind is going to pretty much cover side to side, so there won't be a lot of lost water anyway. Still enough water movement though the media to keep the bacteria happy. They do make a small canister for turtle tanks, but you could use it however you'd like. It's around $30, so not bad to begin with. I'm doing this more for the love of DIY than to really improve on the design or save money anyway. So feel free to take the idea, and re-design and improve upon it all you want!