Thanks, I figured it out that it's enough to mount configmap into clearml pods

Here's my custom-values.yaml

# -- Private image registry configuration
imageCredentials:
  # -- Use private authentication mode
  enabled: true
  # -- If this is set, chart will not generate a secret but will use what is defined here
  existingSecret: ""
  # -- Registry name
  registry: gitlab.my-company
  # -- Registry username
  username: gitlab+deploy-token
  # -- Registry password
  password: token
  # -- Email
  email: my@email

clearml:
  agentk8sglueKey: "key"
  agentk8sglueSecret: "secret"
  clearmlConfig: |-
    agent {
      git_user: "gitlab+deploy-token"
      git_pass: "token"
  
      docker_preprocess_bash_script: [
        "python -m pip install --upgrade pip",
      ]
    }
    sdk {
      development {
        task_reuse_time_window_in_hours: 72.0
        vcs_repo_detect_async: true
        store_uncommitted_code_diff: true
        support_stopping: true
        default_output_uri: "

"
      }
      aws {
        s3 {
            # S3 credentials, used for read/write access by various SDK elements
    
            # default, used for any bucket not specified below
            key: ""
            secret: ""
            region: ""
    
            credentials: [
              {
                host: "minio.my-company:9000"
                key: "clearml-key"
                secret: "key"
                verify: "/etc/ssl/certs/ca-certificates.crt"
              }
            ]
        }
        boto3 {
            pool_connections: 512
            max_multipart_concurrency: 16
        }
      }
    }
agentk8sglue:
  # -- Reference to Api server url
  apiServerUrlReference: "

"
  # -- Reference to File server url
  fileServerUrlReference: "

"
  # -- Reference to Web server url
  webServerUrlReference: "

"
  queue: "4x4090"
  createQueueIfNotExists: true
  clearmlcheckCertificate: false
  volumeMounts:
    - name: custom-ca
      mountPath: /etc/ssl/certs
      readOnly: true
  volumes:
    - name: custom-ca
      configMap:
        name: custom-ca-certificates
  resources:
    limits:
      nvidia.com/gpu.shared: 10

  basePodTemplate:
    volumeMounts:
      - name: custom-ca
        mountPath: /etc/ssl/certs
        readOnly: true
    volumes:
      - name: custom-ca
        configMap:
          name: custom-ca-certificates
    resources:
      limits:
        nvidia.com/gpu.shared: 10