Well, I can't imagine squatting or pressing without my lifting shoes on. I've benched with cycling shoes on (SPD). I deadlifted for a long time with weightlifting shoes on, I have found that I prefer socks. Deadlifting; I think could go either way, depending on anthropometry, flexibility, and preference. If I went to a seminar (which I would like to do some day) I would go with the intent to pass and acquire the SSC certification.
The SS method is a method. I understand that. It's a very well thought out, tried, and backed with results and experience method. There are obviously other methods in the lifting world, some are useful, some are debatable, some are bullshit. Personally, I think deadlifting barefoot is debatable. If your form is otherwise good, I don't see a problem with it.
It shouldn't be the default, but I see it as a legitimate option. I compare this with knee wraps that are considered optional. To me (I'm not a coach, just an observation) knee wraps are over used. They should be optional, but not the default.
Obviously the SS method is for teaching the lifts. When teaching, removing variables is helpful. I see the value in that.