DAE go to The Nether just for the mushrooms?

Seriously, so handy. But I also have another question for you more traveled minecrafters:

I just recently started visiting The Nether. I set up a portal in my main base, puttered around in the underworld for a bit, and then decided I wanted similar access from my secondary base, so I built one there too. This portal is located at least 200 blocks (my best estimate) from the other portal, so I find it odd that when I step into either portal, I come out of the same portal in The Nether, the one that was originally associated with my primary base portal. If I go back through that portal, I come out in my primary base portal again, regardless of which portal I entered The Nether from. Since I travel between the two bases very frequently, my sky bridge doesn't really cut it, but I don't want minecarts running all over my world. I was hoping to use portals as a puddle jumper between my bases, but, as you can tell, it only works in one direction- secondary to primary. Why is this? And how far apart do my topside portals need to be before I can use the underworld as commuter transport and not just to get dumped out in way-the-hell-and-gone on topside?

Here's a pic for clarity: http://imgur.com/NJR7g.png