Ok, I have already proposed that some time ago. You can see the pull request here: https://github.com/pupi1985/question2answer/commit/45a66c6437f42afbf608980b0f92df39ce1451a4
You can move the $this->body_script(); right before the $this->output('</body>'); in qa-theme-base.php. This would be considered as a core hack.
Or you can override the body() in your qa-theme.php moving the same line to the bottom. This would be the best approach.
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