For example, let's say an app has a default keyboard shortcut I don't like. I won't change it. Instead, I'll just get used to it until it becomes muscle memory.
Now the default configurations are my preferred configurations. Of course, there are still a few things I change from the defaults. But since there are so few I can just configure them by hand, because how often am I setting up a new computer? Not very often. And there are so few config changes, it only takes a minute.
The only thing I have to actually sync is my vim config. It's a very small config, but it's still more than nothing. I just store it in a Git repository.