Hi Andy,
Thanks for your input and welcome to ExpressionEngine and the Forums!
When you have templates-as-files, ExpressionEngine manages them with the file “winning” as it were.
When you trigger the Template Manager in the Control Panel or visit the template URI via web browser, EE syncs the file to the database. There is feedback in the Template Manager as to where EE has read the template from.
Make an edit to the template in the Control Panel? EE syncs that back to the file. Granted, the communication about what is happening could be improved, but EE has done this since the beginning.
I want my templates in my version control system because they are code?
EE Devs do it everyday. Generally? When a site is in active development, templates-as-files in VCS. Once the site goes live, they switch to the database.
I do like the idea of a “Master Setting” in some regards, but that presumes a lot on the part of other users… I’ll bring this up with the team and see what kind of traction is gets.
You want me to move this to a more general discussion area for more feedback?
~