Hi Anwar,
Have you done any changes to the web templates and is is done in your development system? If your answer is Yes then all the changes should get captured in your TR automatically when you save your web templates, If this isnt the case then reach out to the BASIS folks.
As you and Brendon have already mentioned the transports can be also captured in RSA1 with grouping objects and select the relevant dependent objects in the hierarchy
Thanks
Abhishek Shanbhogue