It is possible. I'm assuming you know how to get to a tk2dSpriteCollection. At its core -
1. In tk2dSpriteCollection.platforms, add the platforms you need. Order doesn't matter, but the "size (1x, 2x, 4x)" of the first element (i.e. self) does matter so it knows what to do with the other platforms.
2. Call tk2dSpriteCollectionBuild.Rebuild( ... )
That should be it.
Removing platforms on the other hand, is a bit more of a pain, as you will need to delete the unused assets. Refer to tk2dSpriteCollectionEditorProxy.DeleteUnusedData() so you don't miss anything.
If you're planning on doing this, it might be worth investigating adding to the proxy, deleting the bits on the proxy and follow the code path the editor uses, so you won't have to maintain another duplicate set of code, but this in itself will add complexity.