The Allow Skipping User Consent flag is located inside the resourceServers and has the name skip_consent_for_verifiable_first_party_clients. Inside your YAML file it should look something like:
resourceServers:
- name: Test API
identifier: 'https://myapi'
allow_offline_access: false
signing_alg: RS256
skip_consent_for_verifiable_first_party_clients: true
token_dialect: access_token
token_lifetime: 86400
token_lifetime_for_web: 7200