I've posted on this before, but a comment I just left for someone else made me think I might want to take another crack at answering it and see if it's any clearer.
The reason I think passing an amendment to a bill that isn't law yet can work, at least for normal bills (there's an extra wrinkle possible for reconciliation, of course) is that although you can't fix something that technically doesn't exist, you're also technically not fixing that thing until it does. Get it?
No?
It's said that you can't fix the Senate bill because it doesn't exist as law. That's because it hasn't been signed by the President yet. So "it" -- that is, the law as opposed to the bill -- doesn't exist.
But by the same token, the amendments purporting to fix that bill also don't exist as effective legislation until signed by the President.
So what you have before the President signs anything is a bill that purports to establish a health insurance reform policy, and another bill that purports to amend that health insurance reform policy.
Upon signature of the first bill, what you have is an actual law establishing a health insurance reform policy, and a bill purporting to amend that now-established health insurance reform policy.
Upon signature of the second bill, you have an actual law establishing a health insurance reform policy, and then another actual law amending that health insurance reform policy.
Basically, if you think you can't amend a law that doesn't exist because it doesn't exist, you can't also think that an amendment that doesn't exist can actually amend something. Can you?