Hello,
GAP service manages connections, security and bonded devices; GATT service is intended to discover services and characteristics and transferring data between devices. Any modification or exclusion of these services may cause an unexpected behavior depending on your application.
Source code for our BLE stack is not publicly available. Modification of the available BLE Stack is limited to the files and code outside pre-compiled, encrypted libraries.
If the functionality of the stack is not suited for the needs of the prototype you're developing, and the parts you want to modify are not accessible, you would need to develop a custom implementation, but this is really not recommended or encouraged, as for custom implementations, support is limited.
I apologize for any inconvenience this might cause you.
Regards.
Eduardo.