I think Bob should be even more direct about what’s happening. “I know most of the people who disagree with you on this are thinking of X, Y, and Z. My reasons are different. My opinions on X, Y and Z are largely similar to yours. But I’m concerned about ☈, ♄, and ⚗.” I think this approach would do even more than the idea in your last paragraph to make the surprise less jarring for Alice.
I think Bob should be even more direct about what’s happening. “I know most of the people who disagree with you on this are thinking of X, Y, and Z. My reasons are different. My opinions on X, Y and Z are largely similar to yours. But I’m concerned about ☈, ♄, and ⚗.” I think this approach would do even more than the idea in your last paragraph to make the surprise less jarring for Alice.