As long as instruments were used to set it up properly, and it is set up as the book calls for.... it's fine. The exhaust will be hot to the touch. Remember that thing about coal being 70% efficient? That mean if it makes 100,000 BTU's, 30,000 will be going out the chimney.
Two weeks ago the wife & I went to a county tree hugger fair. One booth had a pellet stove outside, running. It was a small one. You could feel the heat blowing out the front vents. Well.... the direct vebt chimney was hanging in the air as if it were going through a wall. I reached and felt the exhaust. Honestly, it seemed more heat was going out the exhaust then coming from the stove! I showed my wife... she was getting all " I want to tell them something's wrong". They were too busy to talk to, but as I told her, I know it's OK. It's normal. When an oil fired boiler is set up it's common for the exhasut to be 325-350*. Granted, that's 10" from the boiler, but I'll bet it still plenty hot by the time it get's out the chimney.