If you go to IM website, you'll see a tune with no mods is the regular tune for $300 something. Then anything modifying the car is considered a custom tune, that's with any tuner. It's basically being tweaked ever so slightly based on the mod your installing and still leaving some safe room depending on the altitude your going to be using the car.
Now a real custom tune is datalogging your runs at the track, then emailing them to IM and him tweaking your tune even more, right down to every 100 rpm throughout the powerband. This way your actually testing the limits in your neck of the woods, not off some dyno that isn't in the same climate as you.