Thanks KieranR
As the SEO-geek I am I pay attention to even very small details. In my experiences it pays! Not only is SEO the sum of all factors but in fact, even very small things can make or break a site in Google. I had cases with clients where litterally one comma the wrong place in some code turned them almost invisible in Google. And just recently I helped a large corporate client get back into Google with their multilingual sites - some minor errors in XML-sitemaps and Hreflang had made Google exclude most of the same language sites intended for different regions. Now they are back 
I think I do have pretty good developers. My own development skills are limited but I know enough to discuss details with my developers about how I want things coded and evaluate it - and JS is often NOT the right solution. Not the least for any elements important for SEO.
We are working on moving one of my clients from another platform to Shopify Plus and will be using a multi-site setup for the two regions/languages they operate in. We are working on a solution matching SKUs (probably appended to product URL’s) to match for creating a Hreflang XML sitemap (maybe with Hreflang Builder - great tools btw). This way we can maintain localized URLs and still have correct Hreflang. Collections we can match manually - the number is more limited and permanent by nature. Also, this solution will not slow the speed on the sites at all which is another of the many “details” I am very focused on.
It would be great though, if Shopify at some point would make a native management of multilingual sites better.
We are by the way also working on a custom solution for product variant - another area where core Shopify could be improved. The current server side and CANONICAL-tag solution is not perfect from a SEO point of view. My preferred solution, in this case, would have been to move the variant selection to the client layer with # but unfortunately my developers have not been able to do that without suffering on the speed - which is not acceptable to me. They are also still working on the best solution to show all variants in collections, and manage order.
No platform is ever perfect but I am looking forward to work more with Shopify. Especially with SO2.0 I think we can do great things. And in contrast to WooCommerce and Magento the user interface for my clients is much better - which is also very important. It is not enough that we - as developers, SEO-geeks etc get what we want. Out clients also have to like the day-to-day work and be able to get it done fast and without the risk of making errors.