Hello,
I am not sure how to explain it. I have not found a topic about it.
I am currently running the native homebridge integration in my Hass. Two in facts : one UI, one YAML.
I want to add a homebridge plug-in (homebridge-harmony - npm). I don’t find how to add this plugin inside the native homebridge. Is it possible ? Or do I need to configure an « external » homebridge ?
Do you mean homekit integration ?
Homebrige is an separate Tool
Yes it’s called HomeKit integration inside Hass.io but it’s based on homebridge, no ?
In my comprehension HomeKit integration is used to make « HomeKit compatible » accessories that are not normally, and HomeKit Controller is used to integrate inside hass.io objects that are already HomeKit compatible. Right ?
After further digging I begin to think that the HomeKit integration is not made with homebridge… Thus I need to install a separate instance of homebridge if I want to expose accessories that are only compatible with homebridge ?
No - HA’s HomeKit support has little to do with homebridge.
If your objective is to bring Logitech Harmony into HA, you would not need the homebridge nor the HomeKit Controller intergration. HA can support Harmony natively.
I do not have my Harmony any more, but I recall when I first install HA, HA could already talk to my Harmony Hub, on the same home LAN, the very first time I boot HA up.
No need to download / install extra plug-in, nor homebridge, nor HomeKit.
I even had an automation to turn on my TV to some specific news channel, when I’m not home but motion was detected on my house.
Not related to Harmony, but…
Also note that HA has the “HomeKit Controller” integration and the “HomeKit” integration.
The first one is to bring HomeKit gadgets (light bulbs or sensors and such) into HA, and the 2nd one is to push gadgets that are already inside your HA to Apple’s Home app on iPhones.
Both have their places - any way read the documents.
Thanks I am making big step forward 
You can do it with the HomeKit integration and the accessory mode