I'm not familiar with the details of the TSA procedure (thankfully, I'm not an US citizen and haven't been there since the whole post-9/11 mess started) -- but I would agree that searching the bag should be done in front of the owner.

That's actually the recommended policy in most cases (not only TSA), for several reasons. One of them is the one you stated; another one is that suspicions related to a particular item can be cleared more quickly by just asking the owner, and if you do it right, you can also get various hints about anything illegal (e.g. the guy is ok until you find the hidden pocket).

There's only one case I know of where searching without the owner's presence would be legitimate -- if the exact testing equipment and procedure must not be divulged, for fear it might reveal vulnerability. This is a form of security by obscurity though, and a sane system shouldn't need that. I'm sure this isn't the TSA's case, but there are cases where it can be an option -- for instance, in an underfunded law-enforcement system that can't afford sufficiently broad testing equipment. In their case, introducing further delay in the obsolescence of their equipment probably ought to be understood. This comes in various other incarnations -- e.g. if you suspect the bag may contain dangerous substances, you typically want to search it in a special, sealed room.

Nonetheless, if searching is done in another room, that's always done according to a procedure that ensures accountability: you ask the owner to tell you what's inside, make a list of everything there, and ask him about the working condition of every gizmo inside. The proper way to do it is with a constructive attitude -- if the bag is stuffed with various items, you assist the owner by taking the items one by one. You don't let him touch them, in case he might sneak up that bag of TNT when you aren't looking, but you help the guy -- if he's got thirty gizmos inside, it's only natural he won't remember them all. But in this case, the search is then conducted by someone else (in order to avoid subjectivity issues -- e.g. the dude has a vintage handheld radio from his grandfather, it's filled with explosive but when you do the search, you test it superficially because it's a vintage radio, what the hell...)