Originally I was thinking, no. But since we will be having new categories for different map sizes instead of just difficulty levels, this will spark more interest in people submitting games played on the other map sizes.
For people playing the GOTM, the map is not known to them, so to them it is a 'random map'. And as long as it meets the criteria (GOTM9 didn't have enough civs). There might be some rule differences, like scout resource denial. Right now, if a player uses it, they would be disqualified from GOTM, but it would qualify for the HOF. So the player would have to decide if it's really worth doing. If he doesn't use the resource denial, of course he would still qualify for both.
And this is assuming that the player doesn't read the spoiler thread until after the game is done. The GOTM's should be turned in somewhat close to when the deadline for GOTM had passed. Some people may not have time in the month to finish the game to meet the GOTM deadline, but would have time to finish it for the HOF. I just don't want to see someone bringing up an old game like GOTM 2.