Can you explain more? I don't see it that way, but it might be we're defining things differently. Milestones are defined in a specific way within the article, and in that way they don't seem orthogonal to me.

Well, firstly, milestones is a standard term and even in this article the author points to the expected definition (reference to Wikipedia article). His "special version of milestones" does not imply another definition, but rather just some specific attributes / requirements / expectations for milestones to be used. Secondly, the author presents project and milestones as a dichotomy ("Most engineering organizations focus on delivering projects. They should focus on milestones instead." - emphasis mine), whereas, in fact, you cannot define milestones outside of the context of a project. Thus, it is not an either/or situation, but rather one where both concepts simply exist. One more note: while both concepts are orthogonal, they are not fully independent; meaning that milestones must belong to a project and a project can have milestones.