The thing is, I'll bet the newly-regenerated stuff will be IDENTICAL to what's there, except with any new features. You may all have noticed that there's no "tearing" and weird joins like in original ragnar? I'll bet that's because of the map seed, which is now stored. If you make a new single-player map, you'll notice you can enter a randomizer seed. Enter the same twice, you'll get the same map twice. Same deal here. So you can trim something out, and it'll come right back EXACTLY the same. That's also why no tearing. It used to be a per-session random seed. Now it's one seed everything's based on, so no tearing.
But that's not a reason not to trim. The reason to trim: if anything's new. I'll bet if you trim a town, come 1.9, a new town will be in EXACTLY the same spot, except it'll have the "flags" set for NPCs to spawn there. Because the seed for the world is the same, thus the random number generator (actually pseudo-random-number-generator) for the world will also "line up" correctly, as long as no differences in HOW the terrain is generated.
Hence why I DO want to nuke the nether, because HOW terrain is generated is also different, at least for the Nether. So it'll be different in at least some respects.