As long as we're talking about one app that is not a periodical or other recurring content, we should --within the bounds of our DPS license-- be able to create multiple folios to customize that one app's media and other features based on the iPad type. IOW if we have to duplicate a folio and create a slight variation to make everything work and look perfect on iPad 3 or later versions, we shouldn't have to pay for another license to do that.
It is not unreasonable at all to make it easy to create the app for each new generation of iPad, based on whatever its resolution and capabilities are. THe number of folios should only dictate the number of licenses when the content in the folios is substantially different. This deal where you design for iPad 1/2 and hope it "looks pretty good" for iPad 3 and beyond is not a solution, it's a bandaid IMHO.