Well let me put it into perspective.
Youre going to be spending about 6-8k on your engine...and 200 on getting it tuned right. Thats like buying the worlds best home theatre system...and having a 13" TV. What's the point?
The EMS systems (meaning the full programmable systems) allow you (or your tuner) to have full control over both fuel and timing...the piggybacks trick your computer into making it do what you want to do rather than it doing it all on its own. Ill use another simile...thats like driving 10 miles out of your way to have someone get you mcdonalds from the store thats 5 miles from your house.
Edit for your last post:
You can have your tuner run two passes if you use crome. Just have him give you both chips. Pop the cover on your ECU pop in the second chip and go. If you run AEM or hondata, just hook up your laptop, load the new map, and youre off. (im constantly leaving out systems like FAST, MegaSquirt and Neptune because of the lack of tuner support in most areas)
Now ill admit, its not as easy as the piggy back systems...but its a better solution, especially as you get into the higher horsepower ranges.