It's the difference between buying an off the rack suit and buying a tailored suit. Ask yourself this: If it has parameters for 2 completely different engines, how tailored can it be to your truck? What happens if you have an air intake, headers, and exhaust? Does it magically have the knowledge and capabilities to know how to correct the fuel/timing tables? No!
It's going to come with some base mapping that will provide some gain on MOST engines. It's far from the optimal setup. Especially if you have other engine mods. A tuner with custom tunes is only like $20 more than the ones you're looking at. Why wouldn't you just spend the extra money, and get the most performance for your $$$?
It makes the most sense to wait, and save the tuner for last though. IF you buy a tuner now with custom tunes, then add more mods, you'll need to get it retuned for the added mods, and that's going to cost more money. Just get all of your other mods done, then buy the tuner with custom tunes. It will give you the most performance for your money, and you'll only have to pay for tunes once, instead of multiple times.