The "Create with shared configuration" currently take over the following configurations when creating a new project:

Permission Scheme
Notification Scheme
Issue Security Scheme
Workflow Scheme
Issue Type Scheme
Issue Type Screen Scheme
Field Configuration Scheme
Request Types
SLAs
Queues
Components
etc..

For Service Projects though it is very convenient to have the below implemented in this function as well:
Portal settings
Customer notifications
Knowledge base
etc...