Refering to this post in Atlassian Answers https://answers.atlassian.com/questions/175568/sourcetree-windows-git-diff-branch1-file-branch2-file?page=1#comment-181747

Add a new Option to the right click menu in File Status. "Diff against branch" and this menu should have a submenu with all the branches to diff against.
Then we should only get the diff between the file in the current branch and the branch clicked in the menu.