Hi cikpis,
There isn't any immediate plans to add import for TexturePacker atlases. That doesn't mean you can't use them though - you can use this runtime sprite collections code to generate sprite collections at runtime, you just need to read the plist / xml data from texturepacker and feed it in here.
1. If you insert the same texture twice into the sprite collection, it won't occupy any additional memory. Matching subimages aren't possible yet due to the overhead in Unity's texture system, it uses a lot of memory already, and this would just increase the footprint.
2. You have to do this manually for now, or with qualitysettings. The main focus of 2D Toolkit 1.80 is having a seamless solution to this, but this is very tricky to get just right because of how Unity works.