custom roms - What's the difference between flashing Gapps on system partition vs installing from play store?

So I'm finally diving into the custom ROM world after experiencing some issues on CM12.1 on my OnePlus One. I have a question though that googling couldn't answer. If I flash only the essential Google stuff : play store, play services, etc, and then install the rest of Google apps from the play store, how would that be different from flashing the full Google apps package? Apart from, of course, using space that would have otherwise been used on the system partition.

I'm especially interested in this as there are a lot of Google apps I never use. I'm aware of the existence of smaller sized Gapps packages but none have the combination of apps I want.