@magnumop you already can (just create a figure / table / equation, then go to the Insert menu and you'll have an option in the "Cross-reference" submenu to reference it). The numbering is updated just like you suggest, and they are exported as LaTeX cross-references (a counter is created for each of the entity types). Section cross-references are not yet there, but is an upcoming 1.x feature.
I've made a note for us to write some support material on the topic of cross-referencing, as it's omitted presently from both the "Getting Started" guide and the knowledge base.
CEO & Co-founder of Manuscripts.app Ltd