I think "just my opinion" means
1. I am not that attached to it and could change my mind if given ample evidence; or
2. It is my personal truth but I realize your experience could just as firmly indicate otherwise, and I respect that, but
3. In any case, I don't feel like arguing the point and will only defend it so far before I lose interest.
I think it also signifies that your response be similarly respectful of individual differences and perspectives, such that you might word a preamble to an argument with "Interesting! I see it a little differently ..."
This leaves room for the other person to save face when you come back to them even if what they said was ill-founded or just plain dumb.
I see it more as a way to indicate the level of intensity the other person is prepared to use in defending his position rather than as a way to indicate that it cannot be challenged at all.