Is it possible to apply the motion tracking data to a new object in a new layer and then output, or export, that layer as an overlay plane (or perhaps in the alpha channel) so that the new object can be interactive (perhaps in a flash swf format)?
I would like to create an interactive layer of objects (created through motion tracking) above a background video layer.
You are severely oversimplifying the matter. Interaction means establishing rules and this in turn requires programming. Ergo, you absolutely cannot avoid Flash and ActionScript. You can certainly do the tracking in AE and then use CS4's "Export to Flash" feature to get the raw setup into Flash, but the work doesn't stop there. For older versions of AE you will need alternate ways to import the tracking data, e.g. by ways of text files, but really, this is much more a Flash topic than one for the AE community, so better ask your questions there.