Vehicle Movement is affected by the terrain, based upon the type of locomotion of the vehicle. If you are playing on a board where the environmental rules include a movement penalty, I recommend defining the penalty and where it occurs.
For instance, our jungle board includes both water and dense foliage. For skimmers this would represent opportunities for bonuses and penalties to their MV value.
Common sense should prevail, and the penalties should be based upon the terrain, not the arbitrary value for foot soldiers.
The Automatic Effects refer to penalties such as reduced visibility, communications penalties, etc.
As usual, communication between the players is essential, and should always take precedence whenever there is a question concerning rules. As long as both players agree to the penalties/bonuses, I see no reason why anything like this would impede a game. For tournament purposes, spell it out prior to the first game.
Does this clear it up?