If we create and save zip in server then it generate relative folder in zip, which is very useless. Zip should work like cpanel.
My suggestion is that you should provide checkbox in popup while compress that 'Do you want to create relative path ?'. If we uncheck this checkbox, then in zip file it should not create relative folder. In this way we can save zip file in server just like cpanel.
I strongly recommend to implement this features. This features may be implement fast (i think). Please check screenshot regarding my idea.