Removing the positive instead of ground does matter for some electronics fabricated in silicon, especially as the miniturization increases and you get further down in utilizing ultra deep submicron technologies. I have not gotten around to writing an exhaustive post of why this is the case, but maybe I will get a chance soon. In the meantime, just let me say the following.
First of all, positive power feeds can have electrical filters on the printed circuit boards which can take care of energy from upstream arcing and sparking propagating down the rails, but, for various reasons, such filters cannot easily be placed on negative. Therefore, designers will normally not go to the difficult lenghts required to correctly put such filters there on negative.
Secondly, different parts of circuits are connected to each other, and if they lose negative they lose their common reference. This can cause momentary potential differences to develop between them, which can result in electrical overstress. Note, we are not talking about large currents here which, of course, will not flow after either terminal has been removed. We also are not talking about long times here (we are talking about MUCH LESS than 1/1000 of a second). Also, we are talking about small charge buildup. CMOS devices can switch extremely fast (thousands of millions of times per second), but to do that requires fabricating them in a way which leaves them extremely sensitive to electrical overstress. It does not take much (or long) for them to fail in various ways, including, for example, gate oxide ruptures if that small charge buildup happens in just the right way.
If the rework instructions from GM says remove positive first, there surely could be great reasons they are indicating this. Don't risk doing otherwise just because you got by with it in the past.