Also when you're learning organic chemistry, where you need to mentally push electrons around molecules which are diagrammed in a highly compressed notation, the negative charges add just a bit more to your working-memory load (which might've already been on edge of what you can handle without dropping something) until you've had enough practice to compile the patterns down.
Negating when you move electrons is just one more step, but so is negation within a complex expression in language or programming, and we do try to avoid piling that up.
Chemistry was my major, and I considered adding this very point, but wasn't sure I could do a good job of explaining what the problem is. You did a great job there ^_^. Yes: there are positive 'holes' that you push a negative number to and then subtract. This is entirely backward and adds considerable difficulty to an already difficult operation.
Negating when you move electrons is just one more step, but so is negation within a complex expression in language or programming, and we do try to avoid piling that up.