The Constitution states that "All Bills for raising Revenue shall originate in the House of Representatives; but the Senate may propose or concur with Amendments as on other Bills." In the months following the passage of Obamacare, many have remarked that while the "revenue bill" may have improperly originated in the Senate, the courts have established the precedent that most origination clause arguments are out-of-bounds because enforcement is the prerogative of the Legislative branch. I would argue that there is a slight difference in this case that makes the origination of the legislation relevant to another key question.
Central to the argument in the Virginia and Florida challenges is the question of whether the individual mandate was enacted under Commerce Clause authority or under Taxation authority. I would contend that the fact that the House acquiesced to pass the Senate bill is compelling evidence that it was the intent and understanding of the legislature to pass a regulation under Commerce Clause authority.
So even if we accept the precedent that the courts should show deference with regard to the self-regulation of the legislature's internal workings, that does not preclude interpretation of legislative intent based on the manner of those workings vis-à-vis the Constitutional design. If such a precedent could be established, it would be an important step towards reestablishing the notion that enumeration of powers means something.