We're trying to create a default manifest that contains a few top primitives scopes that we want the artist to use like
/ASSETS, /CAMERAS, /LIGHTS aso. Is it possible to lock these to always be scopes?
For example if I add a SOP create after our manifest and specify that I want to add my geo to /ASSETS/ENV/ground it modifies /ASSET to become a xform and group and then I have to add a configure primitive node to set it back to type scope and kind none.

There must be a better way of avoiding not constantly having to re-configure the top prims any time something new is created or merged into the flow?
I'm sure I'm just missing something or perhaps misunderstanding something inherent to USD.

I might be wrong but I don't think you're missing anything. Different lop nodes have slightly different approaches to creating missing parts of the hierarchy and/or have lots of knobs to change how things like prim type, kind and even naming are handled. Dropping down those kinds of nodes from scratch each time is almost certainly going to lead to inconsistencies.

The better way imo is to go the HDA route, ensuring a particular workflow or operation happens in a consistent (and maintainable) way.