See my previous comment[0]. That perf test is testing Backbone's use of jQ vs. native DOM, not jQ v. DOM in isolation. I don't trust that there aren't side effects and interactions in the test.
I'm on Mavericks running Emacs 24.3 installed through `brew`. I invoke `emacs --daemon` once when I start work and I have an alias and an Automator workflow to open files in GUI `emacsclient`s. No problems at all. What sort of issues are you seeing?