There's an option to charge "Setup fee" in Pro Sites but the fee is applied to "all or nothing" - so it's either upon signup for all levels or upon upgrade. There's no way to set this to be applied only for selected levels.
The idea is to make it possible to set setup fees for selected levels only. Another idea is to be able to create "custom level" where the price/fee would be set "per feature" (including custom features added, which admin can enable manually) and the total (and activated features) would be based on features selected by the user upon signup.
It would be also great to be able to specify different signup confirmation messages per different levels.