Unlike the original Docker image, here you can use your own configuration.
There is a default configuration, but if you want to override it with yours, then just pass CONFIG_PATH environment variable, containing path to your own configuration, into the container:
docker container run -e CONFIG_PATH=/data/lighthouserc.json -p 9001:9001 -v lhci-data:/data -d ghcr.io/denidoman/lhci-custom-server:main
In the example above we use configuration file placed in /data/lighthouserc.json, so of course you need to create this file inside the lhci-data persistent volume first.