If your knees ache on the interior (where they would touch each other) it's likely you overpronate and have a collpased or collapsing arch. It is possible that you need or usually wear shoes with greater arch support and in these Aldens (which are very flat) you will experience pain.
As mentioned before, the Modified Last does have a high arch, as it is an orthopedic shoe. While I myself have a slight natural arch - it also collapses. Thankfully, I can wear flatter shoes so long as the waist is wider. I find that using heel taps can cause greater knee pain for some people, as they make the shoe less flat and tilt your knees in. Obviously, this is hardly noticeable for some, but for people who are sensitive to changes like that - proceed with caution.