Fix feature flag logging is not working on API

What does this MR do?

We introduced a new logger for feature flag modification, however, Feature API still directly accesses Flipper instance for the modification. Because of that, the logging is not correctly working on production.

This MR fixes the callers to correctly execute the proper interfaces on Feature class and logging the feature flag modification correctly.

Related #276170

Screenshots (strongly suggested)

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• Documentation (if required)
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

Availability and Testing

• Review and add/update tests for this feature/bug. Consider all test levels. See the Test Planning Process.
• Tested in all supported browsers
• Informed Infrastructure department of a default or new setting change, if applicable per definition of done

Security

If this MR contains changes to processing or storing of credentials or tokens, authorization and authentication methods and other items described in the security review guidelines:

• Label as security and @ mention @gitlab-com/gl-security/appsec
• The MR includes necessary changes to maintain consistency between UI, API, email, or other methods
• Security reports checked/validated by a reviewer from the AppSec team