You don't have to edit the config files, if that's what you mean. Generally speaking you should never need to edit any of them except in very unusual cases.

The config files are generally specific to apps and they can get transferred between distributions.

It's actually common practice to take your /home with you too a new distro, it to put it on a separate partition so it's still there after you reinstall the system partition. The app versions might be a little different and sometimes they're may be small glitches when you do that but for the most part it works very well.

The only dot dirs you might care about is .cache which you may want to empty every once in a while (if you run out of space on /home). There's also trash, if you use that, but that usually has its own widget on the desktop so you can explore or empty it.