@GeorgeGkountouras, regarding structural_simplify, there are a variety of ModelingToolkit system types for which it is not needed, or particularly useful. Catalyst.jl, which I work on, is one such case. It generally is used to create purely ODE, SDE, or jump process models, none of which have historically benefited from or needed structural_simplify (even for systems with thousands of states). But I certainly understand your concern with regards to acausal models relying on it.
My understanding is that one of the benefits of the MTK 11 split is that MTKBase would now have a much more flexible system to add compiler passes and transformations (which the AGPL libraries themselves will use to interface with MTKBase). So there is nothing preventing someone else from developing more permissively licensed alternatives to the AGPL components. But of course someone has to want, and have the resources to do, this work. If someone wanted to take on such a project they would at least have the benefit of having access to the MIT-licensed MTK 10 versions of such code as a starting point.
I believe all the AGPL libraries will be accessible to install as normal packages within the general registry, but hopefully @ChrisRackauckas can comment more on that aspect of your questions.
Regarding AGPL implications, as you said speaking with a lawyer is the only response we can give. The Steering Council asked a lawyer ourselves, via NumFocus, for a public statement we could give about the impact of having an AGPL license for the JuliaHub extension library on downstream users and developers, but unfortunately we can not provide any substantive guidance about this (and will not be able to).