Thanks for posting. Lots of stuff to look at here. I've written a short opus for clarity. And I hope that you'll write to me offline, if I miss things that are important to you.
In regards to the whole joule/Moodle model: As you've inferred, joule consists of plug-ins that naturally fit into core Moodle. Conduit (our authentication/enrollment plugin), builds on Moodle's flexibility and offers some features that the other core (16 auth and 15 enroll) types don't offer. And if you decided to stop using Conduit, you have all those other options.
As an admin, you can disable all joule plugins (like Conduit, the grader report, as well as joule reports), so I'm challenging your statement: "but Moodlerooms is making it harder and harder to get just Moodle." The support teams can help you with configuration. We also do a lot of work with our plug-in matrix lists, and configuration teams to clarify what plugins are part of core, community, vendors, or results of our own development, so that our clients can make decisions about the experience of their users. .
joule has a block called the Express theme that a) allows users who know CSS (but not PHP) to create great themes, b) allows users to edit a handful of "template" themes and c) allows users who don't know CSS to change some colors, upload some images, and generally make good-looking sites very quickly. We started using the Express theme about three years ago because we wanted to make theme creation easier and we also had a SaaS hosting requirement that made the uploads of thousands of themes (that were only slightly different) very technically inefficient.
I hear your point that if you wanted to build a manual theme, you would need to build it in the Express plugin, rather than as a regular Moodle theme. NewSchool Learning is great at creating both. They can also easily convert one from another. So if you don't have a theme developer with CSS experience, this is an added expense, but we have done everything we can to minimize migration costs. The rest of a migration is straight forward: we package the Moodle database and data into a package, then we sftp it to its new home. We have had very successful handshakes with Remote-Learner (for instance) who has received the package from one of our former clients, figured out which plugins to install on their end, and pushed the site back into production.
Finally, some words on the business model. Moodle Partners offer a variety of business models to meet the needs of Moodlers. I think the Moodle Partner services are made stronger by our different approaches. Our model (SaaS hosted Moodle with enabled/disabled joule features) is only one flavor. Blackboard liked our model because they saw that our clients like it. Blackboard also liked NetSpot's model which is very different from ours and very cool. But our business models are not changing. As I mentioned earlier, we've been asked to be ourselves, except even more open when we can manage it.