theres alwasy some risk with anything. Look at an intake, a manufacturer can void your warranty if they desire it from that.
Also doing things the old way with distributors and ignition coils have the same level of issues that could arrise but from what i have seen, most people these days are scared of doign software because its not mechanical and as such its just a black box with P.F.M (pure fuking magic) going on inside.
My questions that i have currently asked unichip (since im on hold with them right now) is how did they do specific tunign for CAI/HEADER/Exhaust setups. The deal is that they used a true flow CAI and headers on a tundra.
I just spoke with Frank (i believe his name was over there) and they have impressed me. Not only do they tune for closed and open loops but they do AFR calibrations under dyno conditions and also real world driving. In addition, those that are worried about burning something up, the chip actually has retarded maps that it will switch to to prevent pre ignition and detonation when its is detected. The chip is actually tuned to 92 octane which will allow for 91 or 93 to be used with no issues.
Honestly, as someone that has done software reflashes with bmws for years, i must say that these guys know their stuff. Their R&D is quite exptensive