Mootools squeezebox will remain there, till 4.0. So if you had something working will not stop once joomla makes these changes. Essentially it’s down to 3PD to align the code with the core. That will be extremely easy since all those changes are based on Layouts, so they are totally overridable. As an example: the core will provide all the modals for frond end (protostar template) rendered by bootstrap, some template club might use foundation modal for the same modals since their templates are based on foundation.
Of course as you stated on your comment above this solution isn’t a direct replacement of mootools modal so there might be cases where a designer/dev will have to get his hands dirty and make an override…
I hope that this makes some sense...