The short answer to your question: Yes, it is a waste of money.
The longer answer: In the case of this thread, we are letting the same amount of air IN, while letting air flow more freely OUT. However, if you do the opposite and let more air IN, without allowing for a way to let all the extra air OUT, you are wasting your money. Picture a funnel in your mind. Pour a lot of water in the big end (modified intake/stock exhaust) and it backs up because water is flowing out through a more restrictive opening. Now flow water through the small end (stock intake/modified exhaust) and water flows much more freely with less restriction, but you can't get very much water in there in the first place. Best solution is to modify both intake and exhaust at the same time, and then load a tune (program) designed for that configuration. If you absolutely have to do one before the other, do the exhaust before the intake.