If you buy a ticket with cash, the PDX connections to NRT are often cheaper. This was even true as far back as the PMNW era. The PDX-NRT flight often has better availability for award and upgrade inventory too.

BTW, have you checked what just the PDX-NRT flight costs (in miles)?

Often (but not always) connections are cheaper than nonstop flights because the nonstops are considered more desirable. The connections attract those who are more price sensitive (in terms of elasticity of demand).