For simplicity you are correct. However, those "messaging" protocols are typically only relevant at the IP layer which again for the sake of simplicity typically is understood as the WAN endpoint. When implementing BLE, LoRaWAN, ZigBee you would typically use the read/write/notify/indicate (or equivalent) defined by the standard. The processing overhead of implementing MQTT over BLE would remove much of the benefit of BLE (I won't go into MQTT-SN..) Typically you would transmit local data natively and use a less energy efficient base station (gateway) to reformat the data (JSON/CSV/etc) before publish/POST/etc.
There are so many possible implementations that it's near impossible to set a gold standard.. it's about understanding the tools well enough to pick the best combination for the job.