With leather, it either wins or you do. So if you get a pair of shoes and they fit pretty much correctly, but there is a spot that needs to give, it will either give in a short period of time or possibly end up hurting you a lot. If you are going to get hurt, take it to a shoe guy, and get the spot stretched, end of story.

With saddles for whatever reason, it isn't normally a padding issue, you may be a winner or a looser. If you are going to ride the thing in discomfort for 1K miles, better to mark the sitbones, and upset the surface of the saddle so you are comfortable. That is all you are missing, you need to upset the convex surface into a concave surface, and simply pressing down with a golf ball can do it. Do a very small spot and your seat will do the rest. But if you can develop sufficient pressure, it can take a long time and there is no point to it. I normally break one in in about 4K. Only done 2 for myself, but that is the drill we all use.