Short version:

I need to connect two arduinos to a raspberry pi, over USB, and than have the raspberry act as a gateway over MQTT.
How can I do this? How can I connect the arduinos to the raspberry over USB? I could not find any option for the nodes to communicate with the gateway over USB.

(diagram of what I need to accomplish)
HomeAssistant <-MQTT-> Raspberry <- USB -> 2x Arduino <-GPIO> Switch

Long version:
I'm building a new house, and have every light switch wired to a central location (they are low voltage swithces, connected to the controller of the house, and I have separate controls that actually control the lights). Now there are more switches than GPIO pins on a raspberry, and I'm using two arduinos to connect all the switches.
I'm running HomeAssistant on a raspberry pi, and I'll be using that to keep track of the switch states, and turn on/off lights accordingly.
I thought I could use MySensors to read the GPIO pins on the arduino, and send updates to the raspberry, that would in turn publish those to an MQTT broker. But I can't seem to find any example that uses USB communication between an arduino node and a raspberry gateway.

Can someone help me?
Thanks!