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The issue with STI, and presumably the reason Shimano says don't do it, is that the gear lever takes up a lot of space between the brake lever and the bar. This can limit lever travel, especially if you're 2-finger braking. With slapdash assembly and no attention to maintenance, you can end up with insuffient braking. Shimano have to allow for this as they supply bikes to shops and end users who can't tell their arses from their elbows. With care, you can have Shimano 90mm Mini-V brakes and STI levers and be just as safe as you are with any other rim brake.
alright thanks!