I have the C&L Racer CAI and the SCT/SF3 Tuner and couldnt be happier, granted I'm running a Custom 93 Race Tune, however I started off with a Custom 93 Performance Tune and it was a pretty big difference over stock, if I'm not mistaken if you were to go with the C&L CAI or any CAI that required a tune you would need a Custom Tune anyway, I dont believe you could use a canned tune, your tune would have to be adjusted to accommodate the C&L or any other CAI that requires a tune, hence making it a "Custom" tune.
You can get the C&L Racer or C&L Street CAI and a SCT/SF3 Tuner combo from say American Muscle for something like 569.00 (thats a guess based on memory) and you could have free tunes for life, so say you get gears, or hi flow catted h/x pipe all you have to do is call Bama and they will adjust your tune for the mods you have added for free. Well worth it to me.
I have never ran a canned tune, but from what I have heard they are really not worth all that much, you could get the C&L, Steeda CAI etc....and use a 86/87-89-91/93 custom tune and the car will be perfectly streetable, however the 91/93 Race tunes are pretty aggressive, but once you learn how to drive with the race tune, its not bad at all, a little jumpy at takeoff, but like I said once you get used to it you can take off just as normal as the stock tune.
I have never been into the settings on my SCT/SF3 but like Sparta said above, apparently you can go into the settings on the SCT and adjust for a CAI yourself, I prefer to leave that to the experts personally.
Im no expert at this whatsoever, but I would think if you bought a any CAI that requires a tune and you used a canned tune and went into the settings on your SCT and configured it for said CAI, that would make it a Custom tune anyway, so why not just order the SCT/SF3 with all three tunes (86/87-89-91/93 tunes) already set up for the CAI you purchase?
IMO, its just easier that way and costs no more than buying the SCT/X3 with the canned tunes alone, one other thing I remember one of the guys at Bama telling me is that with the SCT/X3 it comes only with canned tunes, whereas the SCT/SF3 comes with 3 canned tunes as well as up to 3 custom tunes, and they both cost the same, which in my book makes the SF3 a much better deal, more room to expand, if/when you decide the canned tunes just aren't what you want you can load up one of the custom tunes and see how you like them.
I hope this all makes sense, I just woke up and have had only 1/2 cup of java, even if I'm not 100% correct I am just trying to help.
Best of luck
