When the bleeder caps first came out I read to bleed the shock and then pull the shaft all the way back out. This puts the correct amount of air into the shock. I have been doing this since the bleeder caps came out and it works just fine.

The bleeder caps aren't for getting all the air out, they are to make it easier to get the left and right shock exactly the same. It also makes it easier when rebuilding to get the exact same fill.