I think it is safe to assume that the Tony committee will deem them as two separate productions, and will be eligible as two separate productions in performance and direction categories. The exception may be the design categories.
"The Spectacle has, indeed, an emotional attraction of its own, but, of all the parts, it is the least artistic, and connected least with the art of poetry. For the power of Tragedy, we may be sure, is felt even apart from representation and actors. Besides, the production of spectacular effects depends more on the art of the stage machinist than on that of the poet."
--Aristotle