Yes, there are alternatives to editable custom metadata for storing customer-specific configuration:
1. **Protected Custom Settings**: These securely store sensitive data and can be accessed programmatically. However, they lack a built-in GUI for management, so you may need to create a custom UI for updates.
2. **Named Credentials**: Ideal for storing locally generated or per-org secrets. While administrators can view the data, they are suitable for non-sensitive configurations.
3. **Encrypted Custom Objects**: You can encrypt sensitive data and store it in custom objects, with the encryption key stored separately in protected custom settings or metadata. This requires careful permission management and encryption using Apex Crypto calls.
Choose the option that best fits your use case, considering performance, security, and deployment needs.