First of all: this plugin rocks! Take a look Woontrendz.nl which works with this powerful configuration:
Page load time: 511 ms (Tested from Amsterdam, The Netherlands)
Second: I also have a suggestion for improvement of the AUTOPTIMIZE plugin.
The only solution the plugin offers is to place the minified file in the head or the footer.
Why not create an option that allows one to create 2 minified JS files. One for the header scripts, placed in the header, and one for the footer, placed in the footer.