Okay so when I first got him my horse was fairly skinny and did not have much muscle. Saddle fit well, but trainer decided it fit better with a mattes correction pad. Fast forward a year and horse is much fatter and more muscular. He started getting a sore back, so the saddle fit was revisited and we found that there was not as much wither clearance as there had been before.
We now use a borrowed Dover wool wither relief pad. I went out to buy my own, but all of them are very thick and altered my saddle fit too drastically. I realize that they do squish down, but it wouldn't have been enough. Are there any other pads that have the same function as a wither relief pad but perhaps are thinner and are a bit more classic in design? (I don't particularly like the look of the two-toned half pad, but fit is most important)
It's probably not exactly the "wither clearance" that's making your horse sore. Whether the saddle is 1/2 an inch or 3 inches above his wither - your horse doesn't know. What matters is the parts of the saddle that are touching him. Maybe your horse needs a wider tree, or lift at the front if his back has risen due to muscle growth.
Really evaluate your saddle without any padding. If it needs lift here or there, try a thinline trifecta cotton pad with shims or similar. They are fairly thin and won't alter saddle fit as much. You're right in that many half pads are too thick and are simply poorly fitting bandaids.
Look at the angles of the saddle, check for bridging, interference with the shoulder, back panels poking into the loins, etc. Ideally, have a saddle fitter come out if you can.