The ability of the Senate to create "shell bills" stems from their authority to amend bills that originate in the house. They have apparently interpreted that authority as broadly as possible, which means that the ACA, all 2000+ pages, is merely an "amendment" to that original military housing bill (of which no language survives in the final bill). You are correct that this subverts the intentions of the founders in how they organized the Congress, and thus the challenge mentioned in the link I posted.
Nice find. This is a very practicl way to strike down ObamaCare. Much more sure and final than the delay/defund showdown playing out right now.
The constitutional arguments are compelling, since it is so obvious the Founders would never have sanctioned the Senate end-run around the Origination Clause. You don’t need to be a constitutional scholar
Link to pdf, “The ‘Shell Bill’ Game: Avoidance and The Origination Clause”
http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2271261