As I mentioned in my post the Settings under Domain Aliases tab are:
Under the company.com alias, setting the redirect url to http://www.company.com/ takes any traffic to http://company.com/page.aspx and redirects it to the specific URL of http://www.company.com/.
It's catching all traffic and redirecting it to the single page rather than to the corresponding page on the primary domain. I'm just looking to see if there is a Kentico solution as we won't always have control over the IIS settings in some cases.