Thanks for the question. It has been asked previously, you might want to take a look at similar threads:
when-100-may-not-be-the-objective-t1509.htmlhigher-optimization-rate-better-ranked-t1693.htmlThe thing is that WebSite Auditor is just a tool based on relative analysis of things working in practice. As you said, it does not consider inbound links and is a solely onpage optimization tool, so you should combine your work in WebSite Auditor with backlink analysis in SEO SpyGlass.
Another trick is to find the most optimized competitor in each page elements' section — just scroll down to find the list of competitors' page elements, and see who's using the keyword the most. What WebSite Auditor helps you is avoid over-optimization, keyword spamming.