Ok, So Git credentials are present at two locations - 1) outside the agent config and 2) inside it. I updated credentials at both locations and now I'm seeing agent.git_user = <username> in the dump, but I still have the same issue.
` # Set GIT user/pass credentials

leave blank for GIT SSH credentials

agent.git_user=<username>
agent.git_pass=<PAT>

extra_index_url: [" "]

agent.package_manager.extra_index_url= [

]

agent {
# unique name of this worker, if None, created based on hostname:process_id
# Override with os environment: TRAINS_WORKER_ID
# worker_id: "trains-agent-machine1:gpu0"
worker_id: ""

# worker name, replaces the hostname when creating a unique name for this worker                                                                                                                           
# Override with os environment: TRAINS_WORKER_NAME                                                                                                                                                         
# worker_name: "trains-agent-machine1"                                                                                                                                                                     
worker_name: ""

# Set GIT user/pass credentials (if user/pass are set, GIT protocol will be set to https)                                                                                                                  
# leave blank for GIT SSH credentials (set force_git_ssh_protocol=true to force SSH protocol)                                                                                                              
git_user: <username>
git_pass: <PAT>
# git_host: "" `