I would use multisite. As @stagger-lee says, I think the plan is overly complicated. I would use parent/child themes. In some cases I have allowed clients to alter some specific details of a theme, for example colors an such, but ACF is not what I would use for a theme engine, unless you plan on spending many months making it work.
That said, all of what you’re saying is likely possible, with enough work. You could create custom post types on the fly using values saved to some type of options page. This would have an impact on site performance. Using ACF to build custom post types would be very inefficient. I don’t even use plugins for creating post types, at least not in production. I use CPT UI for creating them but always move the registration of post types to code to reduce the number of queries needed on every page load.
