Sadly, Blowfish is right. What looks good with Hornets looks poor with Furies, lousy with Phoenixes and ridiculous with Tsunamis.
Bobboau, though, has proposed a workaround based on spacing the first firepoints widely based on the max capacity of the fattest warhead the ship can carry, then making subsequent firepoints denser and denser so that when you're loading lots of small missiles they're all tightly packed, but with a few large missiles they appear spaced. This doesn't always work either because missile cargo size doesn't correspond directly with the POF size.
Hmm. I just thought of a code opportunity here. See my post in the SCP forum.
BTW, this should be moved.