Absolutely! We call it layer cycling and it's one of Invigorator's really powerful features. I use it to accomplish morphs, deformations and complex motions that couldn't be done any other way. And yes, I've used it to create a 3d coundown as well. (the numbers morph from one to the next).
When you build your Illustrator file, think of it as cell animation... a sequence of images on a sequence of layers. When you import the file into your Invigorator project, use the "import as layer cycling object" option. You'll be able to control many aspects of playback once you've done that.
If you get stuck, post a question and we'l lhelp you through it.