In the initial releases, the first Iron Monger figure had a red chest piece. This might have been due to the various stages of production when Hasbro didn't have enough accurate information to finish the figure... so they went with 'red' for the bad guy.
The second Monger figure came out later and had the Jeff Bridges head inside with the corrected blue chest light.
The new Iron Monger you saw is probably just an adjusted version to be more film accurate. They were able to do this because the toy line was a 'super fist smash' hit. If the toyline failed, there would only be a red variant.
What's more rare? I dunno if I can answer that but I think it's more important to have the one that's film accurate.