MQTT integration with application server

No, what I mean is that the Chirpstack gateway OS itself is flawed for integrations. The configuration files are created on boot, and the only way (to my knowledge) to create persistent changes to these files is using UCI commands
or directly changing the bootup script. Since the integration section of the chirpstack.toml does not have any UCI commands set up, there is no native support for changing those.

The ideal solution is to use your RPI as just a gateway, then have your chirpstack server located somewhere else using the docker or ubuntu install. If you cannot do that, then your only options are edit the chirpstack.toml on each reboot, or find the boot file and edit the script that holds the initial chirpstack.toml configuration. I did the latter once, the only issue is that it won’t persist through updates.