It is indeed an Aikido stance. The front foot is turned outwards slightly to make it easier to turn and to align the hips I believe. The stance can be transitory. I can easily get lower than that - by moving my BACK leg backwards. This seems to make it unstable and move my centre of gravity further back. I want to get lower but keep my weight forward. The only way I can do this is sink my weight forward and dip my front knee - which was my concern. The reason I want to get low is because I am quite tall, and in order to use such a stance to throw someone, it is necessary to be lower than them. Maybe it's my height which is the problem? As for knee walking and seiza - it doesn't seem to hurt my knees - but the tops of my feet (how weird?) - in fact only one other person I've spoken to finds this.
You're lucky! In my case, I've got quite chunky legs, so my knee won't bend beyond 30 degrees. If I try and do it further, and/or put weight on them, then I am simultaneously stressing the knee joint and squashing the muscles.