It's likely the PVR-ATL segment is reserved for more profitable routes or connections that day. It is shortly after the New Year holiday, after all. Searching the one-way from PVR-BOS indicates availability only in Y class from PVR-ATL, so it's probably just an issue of Delta not being able to sell you a connection that is anywhere near as reasonably priced compared to the other options returned. I'm sure you can force a connection through ATL by having an agent manually price it, but you may not like the pricing.

Luckily you are offered three viable one-stop options (two via MSP, one via DTW). This is the benefit of operating multiple hubs, each with service to redundant destinations.