Here are some details, also updated the Github issue:
Need to look at documenting these:
EnableAWSMetering, DownloadExportResults, and BotUserID.
Documented:
EnableSentry - Documented at Telemetry — Mattermost 5.31 documentation. We do not currently list segment or rudder in the config.json documentation page either but do link to the Telemetry docs.
AdvancedLoggingConfig - I believe is documented here: Configuration Settings — Mattermost 5.31 documentation
EnableAskCommunityLink - documented here: Configuration Settings — Mattermost 5.31 documentation
AmazonS3PathPrefix - documented here: Configuration Settings — Mattermost 5.31 documentation.
Internal:
CollapsedThreads - this is for a new back-end collapsed threads feature and currently not available front-end, so all documentation for this will be done once the feature is complete. More details at Mattermost.
NoticesURL, NoticesFetchFrequency, and NoticesSkipCache are not documented separately because they are mainly for internal use. Documentation about Notices here: Configuration Settings — Mattermost 5.31 documentation.
These are just for internal testing purposes: TestFeature, TestBoolFeature.
SplitKey, FeatureFlagSyncIntervalSeconds, and DebugSplit - these are just for our internal feature flag management system (MM-28859 Add feature flag managment system using split.io and remove viper. by crspeller · Pull Request #15954 · mattermost/mattermost-server · GitHub).
Cloud:
These are related to Mattermost Cloud product: CloudUserLimit; CloudBilling; CloudDelinquentEmailJobsEnabled; the entire CloudSettings area, to include CWSUrl.