I have been running BMS JB4 Stage 2 on mine for 6 months and never had issue. I also have it on my 2012 F10 for 2 years already.
I don't have experience on the RaceChip, but based on the reading, it works the same as BMS JB4 Stage 1.
Right of the bat, if you are worry about warranty, MPPK is the way to go.
Benefit wise, BMS JB4 Stage 2 is more flexible as it give you access to custom mapping. Again, I only can comment on the BMS products. You may consult with other forums member that uses RaceChip.
Fuel economy wise, it is depending on how you drive. Personally, after I have the tune installed, I push the car more often while still consuming the same amount of gas. I believe if I drive conservatively, I may gain mpg. But, who can resist the fun of pushing the car when it is much more fun to drive.
Oh, I never took mine off when I bring the car in for regular service, but again, it is depending on the dealer and with JB4 stage 2, you can set it to map 0 which it become invisible to the BMW tool.