I haven't used multiplatform toolkit, but it is clearly very capable as they did SmuggleTruck and that works on many platforms (really well I might add). From the preview videos their approach lets you do a LOT, i.e. reposition, rescale things, use different atlases for different platforms, etc. Having not used it, I can't really say much more about it which you can't learn from the videos, etc.
What I can talk about though, are my plans with 2D Toolkit.
2D Toolkit 1.80 will add the ability to load different atlases depending on platform. Its about 50% done and it does work with VERY minimal overhead, the biggest problems holding it back so far are:
1 - Increased memory overhead building multiple atlases simultaneously. I might work around this for 1.80 by not doing the automatic atlas building part for this version - still undecided about it at the moment.
2 - Resource directory management. Its really hard to manage this as Unity detects ALL resource directories in a project, and we don't really want many "resource" directories - it makes managing builds much much more complicated than it should be.
In terms of workflow, its all done in the asset build stage, and everything else just happens transparently. You need to call tk2dSystem.SetAssetPlatform(...) when the game loads, preferably before loading in any sprites, to tell it which resources to load.
Hope that helps. Feel free to ask if you've got any further questions.