I'm certainly not altering anything in Genesis core.
I'm suggesting that the CSS file you are writing takes precedence over the existing theme's styles.css (what I referred to as default values).
I haven't used this plugin...but at first glance it seems like when you view the style settings in the admin that the existing theme's styles.css aren't accounted for (i.e. your theme's H1 tag is 'green'), but some default style settings from the plugin are being represented (i.e. H1 tag is 'blue').
So it then also seems that if you alter a select few of those settings then the other ones you don't alter may also override some setting you don't want to change (in this example making your H1 headers 'blue', which may not be desired).
Is this how it works, or can you alter settings attribute by attribute basis and not override the rest that you don't want to change?