Same problem I was having the other day, where searching for a PP upgrade itin is showing higher prices to buy Y and upgrade than just to buy Y (which makes zero sense). For example:
It's not as big of a discrepancy as I was seeing the other day on an IAD-BTV trip (where the Y + PP cost was more than double, nearly triple, the cost of F outright!), but it's still wrong.
On domestic flights, there should be zero difference in cost for buying cheapest (non-BE) Y, and buying Y + PP upgrade.