Are you dimensions plans for shop drawings or house and with rooms / etc.?

If shop drawings - dimension to the reference faces of specific timbers / bents. If house plans - dimension to the primary face - if you need a specific dimension in a room (staircase, kitten, bath, etc.) those numbers should drive your plans.

The only time I tend to dimension centerlines is on post locations plans - (and these usually reference back to a primary reference face on a timber) and common pieces when their position marked as centered is not critical.