If it is constitutional, or perhaps I should say if no one with sufficient authority is willing to say that it is not constitutional to "deem" a bill to have passed without actually voting on it, it ought not to be. Hence I propose an amendment, to be added to Article I saying roughly: "No bill shall become law unless the exact same has been passed independently by each house of Congress and then signed by the President, or, failing his signature, being subsequently approved by 2/3 of each house."
Whoever introduced it could say, "it is unfortunate that the Democrats have resorted to Parliamentary casuistry to pass a bill without really passing it. That should never happen again. This amendment is designed to do that," or words to that effect.