I was talking about this with some other commuters, and they pointed out that when riding fast, you might be more focused and alert, not daydreaming. I've also noticed that the faster you ride, the more green lights you catch. Makes sense if the signals are timed for the speed limit. On my experiment days, I seem to spend a lot of time at red lights. I don't like red lights - sitting there waiting to be rear-ended, then trying to clip in and accelerate with a car on your butt, plus yesterday I almost got right hooked by a commercial truck when one of those reds turned green. Feels safer to go through on green.
I do think some of this might be perception, but I also think if you are catching more red lights, that might be the biggest difference. I find the times when stopping for, or accelerating from, red lights to be the ones where I need to be the most alert for danger. Therefore, at least if it was me in this situation, I would feel less safe from going slower, but not so much because of the speed, but for being in more red light situations.
I've riding different sppeds on my commute, I haven't noticed a difference. However, my fast isn't very fast, and the cars are going 40 anyway. I prefer to go a bit slower on my way to work because of less sweat and being more ready to work when I arrive. The time saved getting in the right frame of mind at work more then offsets the couple of minutes I save by going faster. On the way home, it depends more about how I feel.