If the versions are going to look drastically different, it probably won't be easily doable. But the Kindle publishing guidelines have decent examples of how to use media-queries, css and the "display: none" property to handle the differences between the two formats using basically the same source (x)html that you then feed to kindlegen. It creates the hybrid KF8/MOBI that you upload to Amazon.
But creating two completely separate files and gluing the results together when done? That's just not going to happen with the current toolsets (official or otherwise).
By the way, Amazon never really delivers that dual file to any devices... they just split the file and deliver the appropriate portion to the device/app--depending on what it can handle. But you are correct, devices/apps can handle the dual file and read the appropriate one in the event that someone would happen to do their own file distribution, but generally, you're not going to come across many of those dual-format files "in the wild."