The biggest problem with steptronic is the heat that the automatic/torque converter generates. Since the transmission oil cooler share a core with the radiator, you'll likely see water temp anywhere between 10-20ºF higher than you would in an SMG or manual.
Luckily, the M54/N52 are quite reliable in terms of heat management. But I have seen various E9X 328i go into limp mode in high ambient temp situations at tracks with a lot of low speed turns. If you do end up with a steptronic equipped vehicle, I'd invest in a transmission oil cooler just in case.
Otherwise, they are just as reliable, if not for the torque converter and the planetary gearing having a mind of their own.
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