If alternate URLs are not being used, a designer can override term URLs as usual.
If alternate URLs are used, Taxonomy Treemenu provides a Views default template to render them. So you don't need to do anything.
The template renders the View with Taxonomy Treemenu's menu options enabled for sorting and filtering. If a designer wishes to alter the view (the title, say), they can do this by overriding (within Views) the default template.
If using alternate URLs, it is not currently possible to summon a menu's nodes WITHOUT ordering and sorting via treemenu options.