The config parsing code in /usr/src/usr.sbin/pkg/config.c only takes into account the last parsed UCL object. This is too naive and results in unexpected behavior.

For example, having this config

FreeBSD: { enabled: false }
MyRepo: {
   url: my_url
   enabled: false
}

MyRepo: {
    enabled: true
}

results in the last object being used to fill the program's config structure. The url become NULL, causing bootstrap to download from the official pkg repo despite it being disabled.