I think you guys may be talking about the same thing. If you are in a live tourney and get up from your seat, they will take blinds and antes from your stack and deal you in. Your blinds and antes will not be skipped just because you are not sitting at the table.
In some tournaments, they put out full stacks at all the seats at the beginning of the tourney and will take the blinds from the empty seats until the late registration deadline passes. Those who late register are assigned to a seat and may not get a full stack, depending on if their stack has already been forced to pay any blinds. Once the late registration deadline passes, then they will remove all the dead stacks from play.
To answer your question, I wouyld not sit out just because I had enough to make it to the final table. Your goal should not be to just make it to the final table. Now if I got a huge win and had the chip lead and felt I needed a break just to try to calm myself down and refocus, I think taking a self-induced break is fine.
I would most likely get up and just go for a walk, go to the bathroom, etc., to try to clear my head and then get back after a few minutes.