The "Staged" packages are a way of a vendor certifying that they know their tune works and was tested with hardware meeting a defined set of parameters, i.e. if Cobb is going to give you a stage 2 tune, they've tested it with the recommended hardware and confirmed that doing so is safe in 100% of tested cases. Once you step outside that defined hardware configuration, you are moving outside of what they have verified and you may wind up encountering problems. Some changes, like an RMM, really help to mitigate torque steer and the engine banging off the stock rubber mounts (and surprisingly, help the 1-2, 2-3 shifts). Other changes, like the intercooler, keep things safe by lowering intake charge temperatures to keep your car running smoothly. Can you run a tune that stipulates you need an intercooler, without one? Yes - but you are operating outside of the tested spec, so whatever happens is on you. The safest way to do so is to have a cobb accessport so you can log data and get realtime metrics to see how your car is "feeling". You won't necessarily notice knock, but with an AP you'll see your OAR go down, or ignition corrections, etc.
Anecdotally - while my Whoosh IC was on order I installed my Stratified tune anyways. My intake charge temps heated up pretty quickly and I was getting ignition corrections during times when the ambient temp was ~103f. I removed the tune and waited for the IC. Once I received the intercooler and installed it I flashed the tune back on and no longer experienced the negative symptoms - cooler intake charge temps, no ignition corrections, and a generally happier car. When running the tune with the stock RMM, if I hit the gas in second gear it felt like the car wanted to jump into the lane next to me and I could hear the stock mounts thumping around. After adding the recommended RMM - it was nice and smooth, and to this day I murder tires because when they break loose I no longer feel it getting squirrely from side to side, they just break traction smoothly and predictably. I can also see on my AP when I fill up with poopy gas - I'll get some corrections and maybe the OAR will drop, which is usually my sign to drop back to Cobb stage 0 tune until I make some room in the tank and drop 1.5-2 gallons of e85 into the tank, then it generally cleans right up.
TL;DR - just because you *can* do something, doesn't mean you *should*. Yes, they may be making their hardware recommendations to move product, but they also want your car to be safe so they recommend a set of hardware which keeps you as safe as possible while running the tune at that level. Tuners won't be able to sell tunes if people's cars blow up running them, so they encourage you to run their tunes in the safest possible manner.
Also, dermal and big tato exhaust