I think there is some trickery involved for your ’site start’ page so it works from www.domain.com and not www.domain.com/alias. Not sure about Evo though.
What value is showing up in your base tag?
You could also try getting the path from here:
$modx->config['base_path'];
but I suspect you will have the same issue with that too.
I don’t really have any more ideas at the moment I’m afraid
One thing you should be careful to do here is to include a canonical meta tag on every page that points to the equivalent page on your primary domain, as that will avoid duplicate content issues with search engines thinking you have two sites with identical content.