Using truenas have given me little to no understanding of the underlying processes

About 6 months ago I decided to build my first NAS and after extensive research I decided to go with Truenas scale for this system.

While it has been a journey full of learning I feel like I really do not have a solid grasp on what I am doing most of the time especially when it comes to the apps. I have bought a domain tried to setup reverse proxy, and while it seems to work, I am worried since everything is done manually by hand, and when something breaks I will have to setup again by hand. To me this feels like I am doing something wrong.

I was expecting something where I basically setup my entire system in a series of scripts or configuration files, such that I can easily recreate everything from scratch if needed.

Am I doing something wrong?
Or is this my expectations that are wrong?

Your expectations are not quite wrong but TrueNAS is not the system that facilitates this approach to administration. It’s supposed to be managed by the UI which is the entire reason such a product exists in the first place. A plain Linux or FreeBSD system with Ansible would be more like what you describe.

But … if you save your configuration then you can upload it to a newly installed TrueNAS system and you should be right where you left.