Yes, I think you are right as there are probably too many settings to successfully swap out the base store and admin section.
So, I will use a sub-domain that will be kept permanently for admin tasks:
1. admin.mydomain.com - will be the repository/base store.
2. admin.mydomain.com/admin - will be the admin interface.
I will then:
3. Disable products from appearing in the root store.
4. Set up separate stores and websites using sub-directories.
Is this the best way of achieving a stable code base without using our main domain? We currently use our our main domain and it can’t be out of action for any period of time.