I found the easiest way to get the styling for selectize was to remove the uk-input class.
$('.AdminThemeUikit #Inputfield_tags').removeClass('uk-input');
Also, as an update, the new tags functionality for fields & templates does indeed conflict with the module – the result is a JS error which prevents any editing of templates or fields. Anyone using the "Selectize Template and Field Tags" and using the latest dev version, will need to uninstall that module for now, to prevent this error.
I don't see any setting to disable the core text tags inputfield on the tags inputfield, on templates & fields. The only thing i can think of is to somehow destroy the selectize instance that the core is creating, and then the module can do it's usual init; But for now I haven't been able to figure out how to get that selectize instance to destroy it.
Edit: In case anyone is reading this, i just pushed a temporary fix to the module which should prevent the JS errors and the consequent inability to edit templates or fields.