Actually I tested this and it only seems to change the number in the CSS url if you change one of the settings.
So, looks like the answer is yes.
Very nice! It all comes together really well to, as you say, look like it's not Moodle at all (or any CMS really) but a custom hand-crafted website, even though the look continues right into the Moodle courses. The Moodle Blocks in the footer is a particularly nice touch.
One totally unrelated question. I was looking at some of your bullet point lists to see how you were doing the icons and I saw this in the HTML:
<li id="yui_3_9_1_2_1369051526453_77"><strong>4 day</strong> long program</li>
I've seen those yui ids all over the place in Moodle before and never actually found out what they do. Does anyone happen to know? I'm a bit worried that Moodle's spending time adding ids to things via javascript for no obvious purpose.
Oh, and a quick bug report: the dropdown menus worked for me the very first time I clicked, but then didn't work after that and then didn't work at all when I tried another browser.