I don't understand why you insist on putting things in zip files. Git and GitHub really work best with text files. If you move your source code out of the zip file then you can see a diff of the changes made in each commit. The way it is now if I want to submit a pull request for some improvements to your code I have to unzip the source code, make the changes, then rezip the source code. The pull request will not be able to show what changes I've made since you can only see that the two zip files are not identical. You would then need to download my zip file, unzip it, and run a diff on my version vs your version to see what I changed.
putting non-text files in your repository also causes the size of the repository to get big very fast because Git stores the changes to files. If a commit is only changes a few lines in a couple files then that would normally not increase the repository size by much, only the number of bytes to store the diff and the associated commit metadata. However if that changed file is in a .zip file with all the other files then it will take many more bytes to store each commit because it affects the entire .zip file.
GitHub will automatically produce a .zip file of the repository when you click the Clone or download > Download ZIP button so when you download the current repository you end up with a zip file that contains two other .zip files