I like to "bother" people with my "making of". lol Actually, I think it's great to see how it is done. ^^
No. There are at least 50 layers. I never work on the same layer. Too dangerous. xD If you have to change something it's really bothering.
And, the good thing with Sai, is it works like Ps. You can make as many layers as you want, clipping mask, etc. Really useful. :)
Well, Sai is first a painting and drawing tool, like OpenCanvas. So, it can't be compared to Ps for photomanipulation.
But, concerning painting I find it easier to use and more importantly, it demands less disk space. Then, it runs faster, no lag. I had a lot of issues painting with Ps. But, everything is fine with Sai. :)