It's not weird at all actually. If you look at PVR-ATL one way ( forget Boston) on the date it prices at $985 with no available first class for the nonstop. Means they are expecting very heavy well priced loads on the segment so are not opening up the inventory. They are charging less to get you to ATL taking a connection over DTW or MSP

This is not what you'd call married segment logic it's called O&D revenue management. Married segment logic is just the the programming around maximizing network revenue.