In an ideal would it should be simple to add this to the select advanced field type. If an attribute like sortable => true was set along with multiple => true, then the meta data saved would be non-unique and would solve this issue. Then this simple solution (along with enqueuing jquery-ui-sortable) https://github.com/select2/select2/issues/3004#issuecomment-149379355 would allow for these fields to be sortable.
While that works from the sorting perspective, the fact that the data when set to multiple is saved as unique doesn't work. Quickly playing around with the core meta.php files for how data for field types are set. When I forced a multiple advanced selector to single=true data was in fact saved into an array which would of course allow for sorting. I didn't have additional time to play with the JS to force the new index arrays, but I assume it would be close to the way the clone order reindex works.
Seems more plausible to create a new custom field type to get this done (if I ever find the time or the business needs really require it over cloned select fields (which could get very messy with 40+ clones)).