A line-item veto would be a great idea for knocking unrelated garbage like this item out of a relief bill, but it was already shot down by the Supreme Court, and as far as I can tell, there is nothing in the Constitution authorizing such. You either sign the whole thing or veto it or let it either die or become law without acting, depending on when you do that.
A constitutional amendment would be a good idea, but I don’t expect Congress would go for that. Maybe presidents should just let Congress, and the people, know that any bill loaded with junk would be vetoed, but often a president has an interest in a bill loaded with junk, too. It’s a corrupt and dishonest way of making law. If there is ever a convention of the states, this definitely needs to be on the agenda.