Only reason for not connecting the second lead to a battery terminal is to avoid sparks igniting hydrogen gas given off by the battery and blowing it up, nothing to do with voltage spikes. The jumped car has no idea where the negative has been connected, battery terminal or anywhere else that's grounded, it's all the same potential regardless.
Fatal mistake here was to connect the donor battery whilst the donor car was running. Was the BMW's ignition also ON when the connection was made ? Make sure the donor engine is off and the car being jumped sees nothing other than a battery being connected to its battery connections albeit in parallel to it's own battery. This should never damage the cars electronics because it's no different to connecting the battery in the car itself which clearly doesn't trash the electronics on a random basis (would get pretty expensive for the manufacturers if it did). Oddly enough connecting the cars own battery also produces sparks which never seem to cause hydrogen explosions so maybe this bit of advice is excessive anyway.