Why does Project environment has an internal .gitignore?

I am working on a Project (.prj) environment/file with source control. According to the documentation, it is recommended that I use the 'MultiFile' definition file type to avoid merge conflicts, especially when working collaboratively which I am. So, I followed the steps to do it. Whenever I alter(add/remove files etc) something and I go to git bash and check files or when I commit, there are so many files belonging to 'resources' folder AKA project definition files but strangely, when I use the GUI source control section inside the Project menu, only 2-3 files can be seen when committed! This leaves me thinking that MATLAB has internally implemented a sort of .gitignore file to choose what to commit and what not.

The following shows the both scienarios : 1) Project pushed through terminal 2) My forked repo of (1) but pushed the Project with MATLAB GUI

How do I do the same without GUI? This is an issue itself. The Project source control section can only be accessed through GUI which is not very 'MATLAB'

Thanks in advance