Yeah, I wouldn't drill holes to mount it. For one, the housing of the amp (or in this case your powered sub) should not be grounded to the body of the car. This is not always an issue, but it can be the source of humming or whining in the output.
I didn't actually mount my sub, and I certainly didn't remove the seat to install it. I just attached the rubber feet that came with the unit (BASS600) and positioned it underneath the seat. It fits so well that it actually can't go anywhere once you get it in there. The only problem is that it is a pain to get adjusted properly because it is such a tight fit it can be hard to reach the controls, but that's something you should only have to do once.
The only problem I can see with the way I installed it is that it would be easier for someone to steal since it isn't actually bolted down. But if that happens for $90 you can get another one..