Without Qualcomm's help, Fairphone had to enlist the help of the Lineage OS Android community to get the phone updated.
The difference between Fairphone and an aftermarket ROM is that Fairphone is still passing all of Google's CTS tests and officially licensing the Play Store, which is a huge undertaking.
While Apple is a multi-trillion-dollar company with all the resources in the world, Fairphone proves any OEM can offer long-term support if it wants to; they just don't want to invest the time and money to make it happen.