I do not know if I read and understood everything correctly, my last sentence is probably the most important to note.
A free shop system for the general public.
For special needs you can create / buy a module or use the overrides.
For me it is important that the basic system works. Custom things are a different story. Regional larger things may be an additional topic.
To integrate 2 fields for registration, you must either write a module yourself or buy a suitable one or use overrides.
I'm sorry, that's my personal opinion. That's a minor matter. What's wrong with taking notes on your own customizations / overrides or overwriting the affected files directly?
Before each update, you should anyway create backup and test before.
I know, it does not always work. Hence the backup from the backup.
Finally, I would like to add:
- Overwrite the core files and put them into the database works only partially (why and a mandatory field?)
- custom fields ---->
- Login
- account
- invoice
- pdf
- back office
- ....
------> standard theme, panda theme, or warhouse theme etc
-> = does not work in the basic system for everything else, it does not matter