Difficult, as with the depreciation of browser-based reviewing (BBR) from the Acrobat Family, you will only have access to the commenting tools within a browser-framed instance of Acrobat or Adobe Reader when the PDF is in a Shared Review, irrespective of how you create the PDF. Using LCRE to Reader-extend the document only affects the ability of a user with Adobe Reader running in desktop mode to access the complete range of markup tools, and to save copies locally - it doesn't change where the comment data is posted or how the UI behaves in a browser frame.
It's possible to write a plugin (in C++) which manages the back office data transfer of comments in a "conventional" PDF (Reader-extended but not part of a Shared Review), and a number of organizations have done this in-house to facilitate the same mass-volume ad-hoc review system you're looking for, but the plugins are not commercially available as of course they're each designed to work with specific infrastructures. With such a plugin it is currently still possible to activate the comment and markup tools within a browser frame by using a special API function, but we cannot guarantee that will remain possible in future versions as it's tied to the "collab" API system which drives BBR.
If you can store your documents and comments externally, using Acrobat.com workspaces is one option (users don't even need Adobe Reader, they can comment directly within the Flash workspace app) but Acrobat.com services are not available for self-hosting.
The depreciation of BBR was decided after a great deal of debate, and is due to complexities of host environment support which are beyond Adobe's control. It has been decided that Shared Reviews or dedicated plugins are the way to go.
Thank you very much Dave! I guess a custom plugin would not be such a wise investment if the API is likely to dry up on us in the near future.