You can't make an add-on for Calypso without also making it for WP itself -- the key is that WP will be more of a API provider, and the UI will live in Javascript that can live inside Calypso, or embedded in wp-admin before we transition to a full JS interface.

I'm surprise the themes in question are a big deal because (1) they're all GPL and open source (2) they're all available publicly already (3) they're all on the directory or in line to be submitted.

A big goal of Jetpack is to make it smoother and easier for someone leaving WP.com to have the same experience, and using the same theme is part of that. I don't see how making it easier for someone to go from .com to self-hosted is shrinking the market for anybody. :)