diff --git a/doc/manual/generate-manpage.nix b/doc/manual/generate-manpage.nix
index 0b49fac6d..972def69a 100644
--- a/doc/manual/generate-manpage.nix
+++ b/doc/manual/generate-manpage.nix
@@ -70,6 +70,7 @@ let
         * [`${command} ${name}`](./${appendName filename name}.md) - ${subcmd.description}
       '';
 
+      # TODO: move this confusing special case out of here when implementing #8496
       maybeStoreDocs = optionalString
         (details ? doc)
         (replaceStrings ["@stores@"] [storeDocs] details.doc);
@@ -78,6 +79,10 @@ let
         # Options
 
         ${showOptions details.flags toplevel.flags}
+
+        > **Note**
+        >
+        > See [`man nix.conf`](@docroot@/command-ref/conf-file.md#command-line-flags) for overriding configuration settings with command line flags.
       '';
 
       showOptions = options: commonOptions:
@@ -150,7 +155,7 @@ let
             To use this store, you need to make sure the corresponding experimental feature,
             [`${experimentalFeature}`](@docroot@/contributing/experimental-features.md#xp-feature-${experimentalFeature}),
             is enabled.
-            For example, include the following in [`nix.conf`](#):
+            For example, include the following in [`nix.conf`](@docroot@/command-ref/conf-file.md):
 
             ```
             extra-experimental-features = ${experimentalFeature}
diff --git a/doc/manual/src/command-ref/opt-common.md b/doc/manual/src/command-ref/opt-common.md
index 0647228c2..114b292f9 100644
--- a/doc/manual/src/command-ref/opt-common.md
+++ b/doc/manual/src/command-ref/opt-common.md
@@ -203,3 +203,7 @@ Most Nix commands accept the following command-line options:
   Fix corrupted or missing store paths by redownloading or rebuilding them.
   Note that this is slow because it requires computing a cryptographic hash of the contents of every path in the closure of the build.
   Also note the warning under `nix-store --repair-path`.
+
+> **Note**
+>
+> See [`man nix.conf`](@docroot@/command-ref/conf-file.md#command-line-flags) for overriding configuration settings with command line flags.
diff --git a/src/libutil/args.cc b/src/libutil/args.cc
index 00281ce6f..8db293762 100644
--- a/src/libutil/args.cc
+++ b/src/libutil/args.cc
@@ -236,6 +236,7 @@ nlohmann::json Args::toJSON()
 
     for (auto & [name, flag] : longFlags) {
         auto j = nlohmann::json::object();
+        if (hiddenCategories.count(flag->category)) continue;
         if (flag->aliases.count(name)) continue;
         if (flag->shortName)
             j["shortName"] = std::string(1, flag->shortName);