you get less of an arc when you disconnect the negative first, basic electricity.
Which bit of basic electricity would that be?
The "disconnect the negative first" rule applies to removing the cables. (Primarily in a car.) If you're loosening the positive cable clamp with a wrench and the wrench hits some other metal object in the engine compartment, it could be welded in place and the resulting high current flow can well result in serious damage. Thus: Disconnect negative first.
Otherwise: Flowing electricity doesn't know the difference: In each case: One side of the connection has positive potential in relation to the other.
To the OP: Without giving it a lot of thought, and w/o having actually seen your wiring, I don't know as it makes any difference. I'd switch it, tho, purely because it's non-standard and unexpected.