For what it's worth, I don't think the ATS setup will limit you at all with future mods. I'm running a DPS pump on mine currently, and at the low altitude here in Vegas it doesn't even smoke, and I can't get the EGT's up high enough to worry, even loaded.
Back home in Albuquerque, at 5000' elevation, it'll smoke, but the EGT's are still manageable. I usually tow around 7K lbs, but have also used that setup with a slide-in camper in the bed, and other than increased wind drag, the EGT's were fine, even towing through Red Mountain pass at 11000'. I could was able to manage the EGT then with proper gear selection, but if I lugged the engine, it'd peg the temp. I don't think ANY intercooler would have prevented that, and if anything, the increased surface area of another intercooler may have just blocked airflow to the AC condensor and Radiator.
The nice thing about the ATS kit is that it doesn't block the AC condensor or Radiator excessively, and is a bolt-in kit. Same goes for the Hypermax kits. I opted for a pre-fabbed kit for ease of install. I would not hesitate to fabricate my own kit now that I have the time to fuss with it, but there is something to be said for bolt-in-and-go.
One other thing to note, I noticed a 3-5lb pressure drop after installing the intercooler. Even with my wastegate rod shortened all the way, I can't get the boost on my truck over 12psi, with the Aurora 2000 turbo. I've contemplated cutting the rod to shorten it some and see if I can regain the boost, but all the volume makes me worry about not having headstuds and new gaskets...
Ryan