IIRC, something like this process was used to pass the initial bailout bill? Didn’t the Senate gut a bill on the agenda and sub in the text of the bailout bill for the vote? My concern at the time was the Constitution calls for money bills to originate in the House, and this one started in the Senate; but the process circumvented the House origination requirement, I think. I’ll have to do some more checking...
You are correct in your concern, this is what helped defeat the crummy Amnesty bill, Bush made a deal with a bunch of Senators and totally forgot the Constitutional requirement that all bills for raising Revenue shall originate in the House, they didn't use this "amend a bill already passed" maneuver, several members of the House were on record set to kill a law with SC challenge.