Will it still recognise my hardware as being the same

Yes, it will use the same activation slot.

As per thread title, I've just installed Mountain Lion on my iMac as a brand new, clean install to an external drive, with the Lion install still intact (I hope) on the internal drive.

I need to run the Pianoteq installer again, of course, but I'm a little concerned that this might confuse the licence manager. Will it still recognise my hardware as being the same, what with the boot partition being in a different place?