Dot (.) files are hidden files/folders. Config files, for the most part, are located in the users home/.config folder. You should be spending very little time, if any, in that folder.

The standard is to have dotfiles in your ~/.config folder, however not all apps follow that.
Some apps dump their config files in your home, others only have files in /etc or /usr and you have to copy them yourself to modify them

If you use one of the standard graphical desktops (Gnome, KDE, ...) you don't need to explore all of the config files. The most important settings should be in a settings program.

And programs should (mostly) come with sane default settings anyways. Debian adds a few. So the usual way (for beginners) is to start with the defaults and change around stuff once you want to customize something, and starting with the software you use the most (like an text editor, ...). The standard GUI software (like your browser, LibreOffice) has GUI settings dialogues anyways.

It doesn't need to be (specifically) configuration files -- you can add scripts as well. A script that installs every package you need and remove/mask the ones you do not, for example. Which can make a 30 minute long experience become a 3 one.

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.

I wouldn't say there's a place to start. Once you start using programs that are configured through config files, learn about those config files in particular. Eventually, you might find that you prefer editing config files even for programs that have GUI settings - then you dive in more.

Regardless, once your config files become complex enough that you can't quickly rewrite them if necessary, start looking for a dotfiles manager, tracking them in git, backing them up, etc...

i have a git bare repository in my home and use dotbare to manage it.

here you can find all of them https://github.com/simone-viozzi/my-dot-files