I think the biggest difference is that in case of the LoRa Server project, the network-server and application-server are split in different components. This might add more complexity when setting everything up, but also gives more freedom as the network-server part does not have the knowledge about the encryption key to decrypt payload data. It also allows you to swap out components, e.g. provide your own UI and / or node inventory management.
With LoRaWAN 1.1 and the introduction of the join-server, this could also mean that you have one network-server (LoRa Server) and multiple LoRa App Server components running, each App Server responsible for a subset of nodes.
The LoRa Server project was granted financial support from the SIDN Fonds, so I'm able to continue working full-time on the project. Stay tuned for new features