After reading the rules once more I came to realize that the rules say "The entrance to your base can have a maximum of three fading doors." (seen in rule 2.05). This made me think that I can have more then 3 fading doors in my base as long as they are away from my entrance and I had to confirm with an admin that this is not true. From what the admin (Ryder) told me you are only allowed 3 keypads maximum for the entire base.
I think the rules here need to be slightly tweaked to make sure new players do not get confused by this.
Also, does anyone think there should be more then 3 allowed? Personally I think it should be 4, but that's just me :P