I am tempted by your author upgrade to be able to build themes.
However there is one thing missing I think, and that is the option of being able to create a CPT which is unique.
By that I mean that it is a CPT which only can have a single record.
Say for instance that you will like to create a company setting post type, where the user can enter their company name, address etc.
You will only need one of these records, because this is for the company which the website is for.
Think of it as a settings custom post type, which in some sense are theme related, but can be placed in different layouts because it is a CPT.
I would like to be able to create a CPT which is a one record only CPT or unique for settings purposes etc.
If such unique cpt was possible then you will be able to have dedicated themes where the user only had to configure their company information in the wp-admin.
You have a point here and I shared your concern to our lead developer and they will take this as a new feature request.
Please note that how this feature they will implement is still under discussion and once it will be decided you will see this feature implemented in near future Toolset based themes release.