How will the free update to Mountain Lion work?
I suspect it will be serial number based, or model number based.  As the new models will no doubt all have serial numbers and indeed model identifiers (iMac 9,1 for example) that will allow them to clearly identify which machines are applicable, and allow the upgrade as appropriate.

In previous "up-to-date" schemes it has been this way, and not reliant in any way on what is installed on your drive.

If you are transferring to a different boot volume, I would recommend using an image file rather than Time Machine.  You can pick up a USB enclosure for your SSD, image the existing drive onto it, and then simply swap them over - this is how I have done things in similar scenarios.