KTuner Stage 2 is great for daily. I also have the throttle responsiveness and turbo responsiveness set at max. When I flash back to stock for a dealer drop off I feel the car is almost un-driveable I've gotten so used to it.
As far as damage goes, nobody can really say yet. We will need 75-100k+ miles on these tunes to really know. According to KTuner, the Stage 2 base tune is still very conservative with lots of room left. I'd be more concerned about a custom tune pushing the limits of the components more than their base tunes.
For manuals, the only factor I see possibly being an issue is the clutch. Tuned 1.5L's are already having clutch slippage issues. So, worst case you may need to upgrade to a better clutch if you have the 1.5L. For the 2.0L, I have seen no evidence of the clutch giving out early since it's stronger than the 1.5L's clutch. However, I have also not seen any torque ratings published for it either.
For automatics, Hondata is being cautious with the amount of torque they are putting out
. I can't find the article right now, but Honda released specs saying the 10AT has a maximum rating of 295ft-lbs. Hondata is limiting the torque output for the automatics to around 300ft-lbs because of this. On the manual transmission, they are putting down around 330ft-lbs.
Point is, the tuners are cognizant of the published limitations but it will take years to really know what effect, if any, the tune will cause.