When you redownload a now-deleted-preloaded app, it actually downloads it. You can see the progression in the App Store. Which makes me think that Apple actually removes the App package from the phone.
This is how disabling apps in Android works also. There is a baseline version baked into the ROM, but any updates are installed into normal memory. Disabling the app removes the updates from normal memory, so when you enable the app again it will (likely) need to update.
When you redownload a now-deleted-preloaded app, it actually downloads it. You can see the progression in the App Store. Which makes me think that Apple actually removes the App package from the phone.