Well, the meta setup allows you to have separate tags on a single site because on the PPTM UI level you kind of have 2 different containers. They are later (when published) joined together in a single tag tree but I’m not sure if that’s a problem.
What I usually do in case there’s a need for both specific views (seperate sites/domain) and a cross-domain tracking view is create a single tracking code containing 2 addTracker methods. One for the separate site and one for the cross-domain one.
I have tried both having a single Piwik PRO Tag Manager container for all of the websites and using a meta setup to keep the separate containers and deploy the “double tracker” on each of those websites with ease. The second method allows you to keep all of the tags that need the per site separation and deploy additional tags on top of that. There’s a short description of this method here.
I usually stick to running a single tracking code when splitting traffic into 2 different sites but you could try keeping all of the default tracking tags and adding the cross-domain tracker through the meta setup. This is not something I’ve tried but I think it could address the tracking tag separation need.
Using custom code is for sure more complicated than using UI to configure stuff like this but it’s still possible. Maybe I’m missing the point here but the attached image from your opening post looks very similar to what I’m describing above.
I agree it could be simpler when it comes to the implementation but this approach has some drawbacks (Simo has a cool article on this topic).