Resolve "Projects API: filter 'with_issues_enabled=true' returns projects with 'issues_enabled=false'"

What does this MR do?

#34055 (moved) Fix the Projects API returning projects when filtering with issues_enabled=true if they have the issues feature set to private.

Are there points in the code the reviewer needs to double check?

The same probably also has to be done with with_merge_requests_enabled, but I did not include it in this MR. I can change it if needed.

Why was this MR needed?

#34055 (moved).

Screenshots (if relevant)

Does this MR meet the acceptance criteria?

What are the relevant issue numbers?

Closes #34055 (moved)