I would suggest to separate out the Ecom capabilities from all things Customer perspective like themes and other things.

Technical architecture
It would make development a lot easier and new developers would easier get a grasp of the platform and how to make changes.
Companies and individuals interested in the ecom would be able to use it with other CMS systems a lot easier.
Security would be increased since it is easier to separate it from the webfront (instances) by breaking the two parts apart.
The ecom and the webfronts would scale more cost efficient since the webfront (CMS/Themes) requires many small instances and the Ecom primarily few and large instances.

Market analysis
So, even though a slight overhead in architecture that overhead of separation would benefit so many areas and be quickly gained back. The overhead would primarily effect very small implementors focusing on click to create and plugin usage but the competition on that market is today completely owned by SaaS providers like Shopify.
The change would allow for large scale enterprises to invest in the platform and the platform to truly compete with SaaS providers like CommerceTools, BigCommerce etc. since it's open source and scale much better on a cost perspective, lower the startup time by minimizing commercial and legal agreements.
So much to say about it, hapy to hear what other think of it?