Summary:

Custom field configuration is not retained when being migrated from team managed projects to Company managed projects.

Based on the following documentation Migrate between team-managed and company-managed projects

Custom fields: If you use custom fields in your team-managed project, a Jira admin needs to recreate the fields and add them to screen schemes and field configurations in your company-managed project. Custom field data will need to be recreated, otherwise it will be lost. 

Above is applicable for Global custom fields.

Suggestion:

Ability to retain customer field value for custom fields that are created from the team managed projects ( system fields ) when being migrated to company managed projects.