Commit of a merge commit diff doesn't show all the changes

In gitlab-org/gitlab-ee!3361, we were quite confused by the output of:

https://gitlab.com/gitlab-org/gitlab-ee/commit/05b572d974bde1ee390e9a46d5a9238d89f5a8f2

As you can see, the merged branches are:

• gitlab-org/gitlab-ee@078f29f6d0c
• gitlab-org/gitlab-ee@4980f36e1b7

The UI doesn't show a number of changes that git diff 078f29f6d0c..4980f36e1b7 has. For example, it omitted lib/gitlab/github_import/client.rb completely:

diff --git a/lib/gitlab/github_import/client.rb b/lib/gitlab/github_import/client.rb
index c1c338487a7..844530b1ea7 100644
--- a/lib/gitlab/github_import/client.rb
+++ b/lib/gitlab/github_import/client.rb
@@ -38,14 +38,7 @@ module Gitlab
       #            otherwise hitting the rate limit will result in a thread
       #            being blocked in a `sleep()` call for up to an hour.
       def initialize(token, per_page: 100, parallel: true)
-        @octokit = Octokit::Client.new(
-          access_token: token,
-          per_page: per_page,
-          api_endpoint: api_endpoint
-        )
-
-        @octokit.connection_options[:ssl] = { verify: verify_ssl }
-
+        @octokit = Octokit::Client.new(access_token: token, per_page: per_page)
         @parallel = parallel
       end
 
@@ -170,27 +163,8 @@ module Gitlab
         octokit.rate_limit.resets_in + 5
       end
 
-      def api_endpoint
-        custom_api_endpoint || default_api_endpoint
-      end
-
-      def custom_api_endpoint
-        github_omniauth_provider.dig('args', 'client_options', 'site')
-      end
-
-      def default_api_endpoint
-        OmniAuth::Strategies::GitHub.default_options[:client_options][:site]
-      end
-
-      def verify_ssl
-        github_omniauth_provider.fetch('verify_ssl', true)
-      end
-
-      def github_omniauth_provider
-        @github_omniauth_provider ||=
-          Gitlab.config.omniauth.providers
-                .find { |provider| provider.name == 'github' }
-                .to_h
+      def respond_to_missing?(method, include_private = false)
+        octokit.respond_to?(method, include_private)
       end
 
       def rate_limit_counter