While builtin containers are indeed containers, I assume that you're asking about OU's since they are one of the 3 container types that GPO's can be linked to.
In this case, you can create your own OU's and put them in just about any parent container that you like. Link your GPO's to your OU's and not the builtin containers and your GPO's should work.
I'm fairly sure that none of the builtin containers can be deleted, but I haven't tried to confirm this.
Yeah I've always just been told it's to prevent you really screwing up the AD (although this is still easy to do in many other ways ). By not allowing you to delete them or apply GPOs to them it preserves a 'safe' area within AD. It also provides a common factor across all AD installations so if say an application install creates users (e.g. SMS) they can code the location of this rather than rely on the user entering the correct LDAP distinguished name during installation.
they're also what remains of the local SAM, and if ever you downgrade your DC, maybe their content will be there when you emerge the other side of your dcpromo....
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