I'd like to bump this post, because I've also looked for a solution. No luck though.
I've set both hot_exit / remember_open_files to false, besides liking it that way, I also have the idea st2 is booting a bit faster. But I do want the last state of my project files when I open a project. Setting these (project based) options doesn't seem to work. "Close project" does work, but is not the best solution.