I think 2D Toolkit could work for you, but I'll go through each of your points to tell you at least what to expect.
2D Toolkit can't use TexturePacker spritesheets, so you'll need to import from individual sprites. Regularly spaced tiles work too. PNG transparencies should just work - you can test this by simply dragging your texture into unity, if the transparency appears correctly in there (it should), then 2D Toolkit will read and use it fine.
I don't understand your question about colors/transparencies changing. The example you've shown is predominantly in black and white, so where do the colors / alpha come in? Our built in shaders allow you to tint instances of sprites so you can say make the hat 50% visible no problem at all without messing about with the atlas.
Colliders can be generated automatically per sprite, and then should follow the animation, but the only type of collider which you can animate like this are boxcolliders to avoid creating and deleting components dynamically. In the current version you can't rotate box colliders relative to the sprite so that limits what you can do.
The environment layering should just work, can't see any problems with that. You obviously understand that you'll need multiple layers for these textures / shadows / etc. Shouldn't be any problem. You simply position these at different z layers, and it'll just work fine. Its probably best to avoid perspective cameras, and favour the parallax script in our private support forum should you need that. It looks like you may not from the images though.
One thing you didn't mention was what platform you're targetting. The number of layers you're describing there should be fine on PC, but I'd be very cautious trying anything like that on any mobile platform.
Hope that helps, if you have any further questions, feel free to ask.