Not looked into valid tags on Plone 5 (yet), but Plone 4 TinyMCE configuration was also looking into filter settings: it was dynamically adding valid tags reading from the Plone filter configuration.
Are you sure it's not working? Can you inspect to see if the TinyMCE extended_valid_elements (or simply valid_elements?) is provided in the JSON configuration?
It does't seem a thread cache issue. I tested changes after a Plone 5 but new tags are kept only with TinyMCE/JavaScript disabled.
I checked the Plone 5 source but I don't find a point where safe_html contiguration is read anymore. I fear this feature has been lost in the mockup migration.
It was one of the most buggy and cumbersome features that was attempted to be implemented in the previous tinymce implementation and no one worked on re-introducing it. IMO, it's better to just let the safe transform clean the markup on the way out than tinymce screwing up your markup all the time because of the configuration.
@vangheem but how fix the issue reported by @alessio? TinyMCE is still cleaning the code client side, so there is no way now to introduce additional tag, isn't it?
You can check the configuration on the data attributes of the raw html output.
What you can do is go to the tinymce configuration in site setup -> Advanced and provide a json config of configuration you'd like to override for tinymce.