Thanks Brian for the reply. I am aware of all those things but the points is "when you create the new user database without any specific configuration, it should get created as per model database setting" but in this case it is not.

The steps to replicate the issue :-

1) Modify the model databases's data and log file size to something else.

2) Now create the database via plain tsql as "create database test" and this doesn't create the database as similar to model.