SEO software for evaluating sites is CRAP! Please understand I amnot being critical of you your services or your site here, I am just pointing out the following. The 'score' you talk of will be using things like keyword density, prominence, etc, which is ALL almost uselss these days.
Also SEO software can ONLY evaluate individual pages, which again is useless.
On 'PAGE' seo is pretty much limited to getting the title correct, and the proper use of heading and layout sprinkling the key phrases and related words.
'SITE' SEO is all about the architecture, the relationship and interlinking of the pages and the control of content across the site. Also inbound linking is a key to it all and software can't understand semantic relevance, so is pretty much useless at this also.
PLUS they comment on stuff on page that most CMS's & Shopping carts will NOT allow you to control.
Web CEO (and some others) is VERY good at running reports though which is what i use it for (and nothing else) !