Sluggo said:

Unless Vader is arriving "covertly" as it were. Jerjerrod was surprised at his arrival.

This is true, but it need not be that surprising IMO. People really like the idea of using the Executor. It seems its popping out of hyperspace and a shuttle immediately departing is still plenty surprising.

But his covert arrival is all I can think of as the original reasoning, though I don't know why he would be so cautious. Often these things are done with great pomp.

EDIT: On top of this, people voted to make Vader tougher, but we weren't sure how to do it.. This gives him a more intimidating presence in the film, as does the reincorporated Jerjerrod choking scene with a stronger line instead of that spoken by Prowse.