As with the "Jules Verne" and "Samurai" scenarios included with Fantastic Worlds, you can set-up multiple scenario files saved with the extension .alt, and the computer will randomly select one of the files when you load the scenario.
This is just off memory. I also think you could either set a corresponding introductory or events.txt, but I'd have to check that.
Basically this is good for altering starting positions, no. of units, etc.
Other than that, no. You cannot play a scenario and have a random map each time, for the simple reason that the map comes first. The scenario is then constructed based on that.
------------------
"The man who can smile when things go wrong has thought of someone he can blame it on"