I don't quite know how your post went unanswered for so long; however to quickly answer your question why would something like that have to be created in Swift3D when it could be created in 2D with good gradients and whatnot?
Swift3D would do what you're asking - the holes would have to be created with some mesh edits since booleans are not supported even in version 5.0 - but what all are you wanting to do with that would require 3D?
You are absolutely right, I gave up on the 3d version of it and went with 2d photoshop and brought it into flash. It works, so I didn't need to mess with Swift3D at all.