Well that's the problem though, the bill isn't transparent enough when you have things not pertaining to the main subject added, line item veto or not.
If it's about subject "X," everything in the bill should relate to subject "X." Then you don't have things getting passed or not passed just because of other items on the bill. It would simplify things so everyone could understand it, while also getting rid of "surprises" later on (earmarks and pork), as you mentioned above.