Probably a stupid question but with competitive symetrical maps with clear red and blue sides, is it acceptable to colour the centre of the map with a different colour? Rather is there a specific rule with this where if you wish to use a 3rd colour it must be green or it must be yellow, can't be orange/ purple etc?
Neutral color can be anything. Just make sure it doesn't get in the way of callouts. Most maps are divided into quadrant colors b/c it's the "sweet spot" for the number of callouts. Red, blue, green and gold/yellow are the most common since they stand out and are unique from one another.
I generally recommend leaving the middle of a map uncolored. It's usually not necessary for callout purposes since people will just call out 'top mid', 'bottom mid', etc. If you think it's necessary, you can pretty much use any color except red or blue. There are no standards in place that state you should use a particular color in the middle portion of your map.
^^^^ This, and since halo 3 we've been using the custom power up and teles to show the color. If the middle structure connects to one of the colored bases, you might as well leave it that color. If not or it connects to both, i'd recommend just leaving it plain so colors don't clash and it can easily be called "top mid", "mid" etc..
I usually make mid purple but sometimes I feel that too many colors make the map look odd. Like Fruit Stripe gum.