I'd like to keep the ground as short as possible.
That can be a mistake. (And, I didn't say is, but can be.) If there is any voltage difference between earth at the back of the car and earth where the HU connects (and there will be), this can be seen as noise on the input to the amplifier. Then, it comes down to the frequency spectrum of that noise, any attenuation on the input (to what extent you are using high level inputs) and the response of the sub at the frequencies in question.
So, once you;ve got it hooked up, have a listen and see if any strange noises (ignition/injection, alternator, switching on and off, eg, the heated rear window, etc) are making their way through to the acoustic output. If not, you are good to go, if so, you've got a bit more to do.
The 'electrically correct' place to connect is as a start ground, to the same place that the HU gets its ground, but there may well be other places that work, depending on how critical you are and the characteristics of the various bits in your system.