I don't have any pics. But yes, I meant put the car back together with everything in place.
I did the clutch on my '05 a few months ago. The bleeder is on the little "block" where the clutch line connects at the transmission bell housing. When I bled mine, I didn't touch this fitting at all. The only thing I did was fully flush and bleed the brake system first (to get fresh fluid in place in the master cylinder and all the brake lines) and then I pumped the brake pedal slowly for about 5 minutes.
When I started, the pedal when straight to the floor with no real resistance. But, after a minute or so, it started to get a bit of resistance towards the bottom of the travel. This built up as I slowly pumped the pedal until it had ALMOST normal resistance all the way to the top. After 5 minutes, the car was drivable, but the pedal was not 100% normal. However, the next day when I took the car out, the pedal was exactly like it was when I first bought the car.
So, the reason the factory removed the bleeder nipple is it really isn't needed and it probably has lead to some other problems (like leaks) instead, so it was better to remove it and call it done.