Personally, I think this has been one of the more useful threads recently. Pegleg made some very good points a few pages ago about why it might be a bad idea, which are worth thinking about.
I don't think it'll change my overall approach to these situations, but I have more to consider now. Basically to be careful because there are ways you can screw it up - if you get it wrong it could end up undermining your authority (players thinking you don't know what you're doing) and make you look a prize tit ("scrum here or penalty there?" "where's the penalty ref?" "over there, x meters in from touch and y meters back. No, not there, over there" "oh, we thought it was there, can we actually have the scrum?"). As I say, I don't think I'm going to stop doing it - I'm just going to be more careful.
Though I didn't hear the ref ask in this clip, I think I can see why he offered the choice there: the Brumbies had just had a very strong scrum, so he was probably thinking "scrum V is probably advantage if they're going to scrummage like that, but it'll look a bit weird if I don't go back for the penalty, so I'd better check". And it was as well he did so.