AlterBrains

So now that I have this extension, I have the choice of using Joomla's registration or PhpBB.

I know with PhpBB you can have custom fields be a part of the registration. With something like Community Builder or JomSocial you can also have custom fields.

So my questions is what's the pros/cons in using one registration system over the other?

No difference from techical point of view, you can just choose any you like more.

Is it ok to use both of them?

Yes, it doesn't matter which registration form to use.