What's the difference between flashing Gapps on system partition vs installing from play store?
You can go ahead and flash Gapps Pico (Google system Base, Google play services, Google play store) which contains apps that are essential for Google Play-store support. You can later install other Google apps which fit your need.
You can refer to the image below to find if there is any package that fits your need.


Click to enlarge. source:androidrootz   

Alternatively, if you are not satisfied, you can install the Complete Gapps package and simply uninstall whichever apps you don't need by Root Uninstaller