Sorry, I don't understand. What do you mean by "give Apple/Google root access"? I've always assumed they already have that.. if no, how does OWS give them root access?
OWS doesn't then allow you to use their servers for routing/discovery etc - so you need to run your own servers, and set up a different network that cannot federate with the one users of the Google Play Appstore version of Signal use.
If you do that, and install eg. the F-Droid store, you've now given another actor (the F-Droid store) access to your phone. OWS argues that in general you're less likely to manage to run a safe, patched system this way.
? That's a misunderstanding. You can of course use the official servers with your self-compiled version. (side note: I also don't think your phone needs to be rooted for this)