WE are looking into doing a second domain with our Magento store and this would have a drastically different checkout behavior so I wanted to see if its possible to have a completely separate configuration on the backend for the second domain.
It really depends on which settings you need to tweak. Each configuration option has what's known as a "scope". The three possible scopes are:
- Applies application wide
- Settings can be changed for each Magento website (e.g. foo.com and bar.com)
- Store View
- Setting can be changed at the store view level (e.g. English version foo.com vs Spanish)
In the example above it would be possible to configure the Quote life time for foo.com and bar.com differently but not for each localized version of the sites.
If you're more concerned with checkout flow on the frontend side then that would be mostly a theme related configuration. Themes can be configured down to a store view level.