We run some commands to setup the environment, that you can see in our Dockerfile. It in turn, runs the onion-feed-setup.sh script to setup our feeds. We then rely on the build system configuration that's stored in .config.
If it seems that your build system configuration isn't matching the firmware that we build, it might be because when ./scripts/feeds is run, it overwrites the .config file. To remedy this, you can just run git checkout .config (assuming you're using our github repo or docker image).
As for packages failing to build, we've seen this happen as well but only when running our Docker image on a windows machine. If the Docker image is running on Linux or Mac, there's no issues. (Haven't had the cycles to figure out why it doesn't play nice with Windows)