Based on your description, I understand that you want to users can start the workflow manually meantime cannot check in and check out files manually.
Per my knowledge, if a user with permission to start the workflow manually, the user also can check in and check out files. There is no option to achieve your requirement.
As a workaround, you could create an automated flow or workflow to check in and check out files. Then grant users with read permission for the document library.
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