diff --git a/mypy/build.py b/mypy/build.py
index 11d826cf9e9f..a0f80f365722 100644
--- a/mypy/build.py
+++ b/mypy/build.py
@@ -131,7 +131,7 @@
     from mypy.report import Reports  # Avoid unconditional slow import
 
 from mypy import errorcodes as codes
-from mypy.config_parser import parse_mypy_comments
+from mypy.config_parser import get_config_module_names, parse_mypy_comments
 from mypy.fixup import fixup_module
 from mypy.freetree import free_tree
 from mypy.fscache import FileSystemCache
@@ -478,6 +478,7 @@ def build_inner(
             dump_timing_stats(options.timing_stats, graph)
         if options.line_checking_stats is not None:
             dump_line_checking_stats(options.line_checking_stats, graph)
+        warn_unused_configs(options, flush_errors)
         return BuildResult(manager, graph)
     finally:
         t0 = time.time()
@@ -502,6 +503,19 @@ def build_inner(
             record_missing_stub_packages(options.cache_dir, manager.missing_stub_packages)
 
 
+def warn_unused_configs(
+    options: Options, flush_errors: Callable[[str | None, list[str], bool], None]
+) -> None:
+    if options.warn_unused_configs and options.unused_configs and not options.non_interactive:
+        unused = get_config_module_names(
+            options.config_file,
+            [glob for glob in options.per_module_options.keys() if glob in options.unused_configs],
+        )
+        flush_errors(
+            None, ["{}: note: unused section(s): {}".format(options.config_file, unused)], False
+        )
+
+
 def default_data_dir() -> str:
     """Returns directory containing typeshed directory."""
     return os.path.dirname(__file__)
@@ -3774,7 +3788,7 @@ def load_graph(
                 manager.missing_modules[dep] = SuppressionReason.NOT_FOUND
                 # TODO: for now we skip this in the daemon as a performance optimization.
                 # This however creates a correctness issue, see #7777 and State.is_fresh().
-                if not manager.use_fine_grained_cache():
+                if not manager.use_fine_grained_cache() or manager.options.warn_unused_configs:
                     manager.import_options[dep] = manager.options.clone_for_module(
                         dep
                     ).dep_import_options()
@@ -3824,8 +3838,8 @@ def load_graph(
                     graph[newst.id] = newst
                     new.append(newst)
     # There are two things we need to do after the initial load loop. One is up-suppress
-    # modules that are back in graph. We need to do this after the loop to cover an edge
-    # case where a namespace package ancestor is shared by a typed and an untyped package.
+    # modules that are back in graph. We need to do this after the loop to cover edge cases
+    # like where a namespace package ancestor is shared by a typed and an untyped package.
     for st in graph.values():
         for dep in st.suppressed.copy():
             if dep in graph:
diff --git a/mypy/ipc.py b/mypy/ipc.py
index 0bafc2f7a474..29710cd57a91 100644
--- a/mypy/ipc.py
+++ b/mypy/ipc.py
@@ -53,9 +53,8 @@ class IPCBase:
     This contains logic shared between the client and server, such as reading
     and writing.
     We want to be able to send multiple "messages" over a single connection and
-    to be able to separate the messages. We do this by encoding the messages
-    in an alphabet that does not contain spaces, then adding a space for
-    separation. The last framed message is also followed by a space.
+    to be able to separate the messages. We do this by prefixing each message
+    with its size in a fixed format.
     """
 
     connection: _IPCHandle
diff --git a/mypy/main.py b/mypy/main.py
index 23953c606d6a..acc27f1806b7 100644
--- a/mypy/main.py
+++ b/mypy/main.py
@@ -23,12 +23,7 @@
     sys.exit(2)
 
 from mypy import build, defaults, state, util
-from mypy.config_parser import (
-    get_config_module_names,
-    parse_config_file,
-    parse_version,
-    validate_package_allow_list,
-)
+from mypy.config_parser import parse_config_file, parse_version, validate_package_allow_list
 from mypy.defaults import RECURSION_LIMIT
 from mypy.error_formatter import OUTPUT_CHOICES
 from mypy.errors import CompileError
@@ -221,26 +216,6 @@ def flush_errors(filename: str | None, new_messages: list[str], serious: bool) -
         blockers = True
         if not e.use_stdout:
             serious = True
-    if (
-        options.warn_unused_configs
-        and options.unused_configs
-        and not options.incremental
-        and not options.non_interactive
-    ):
-        print(
-            "Warning: unused section(s) in {}: {}".format(
-                options.config_file,
-                get_config_module_names(
-                    options.config_file,
-                    [
-                        glob
-                        for glob in options.per_module_options.keys()
-                        if glob in options.unused_configs
-                    ],
-                ),
-            ),
-            file=stderr,
-        )
     maybe_write_junit_xml(time.time() - t0, serious, messages, messages_by_file, options)
     return res, messages, blockers
 
diff --git a/test-data/unit/check-incremental.test b/test-data/unit/check-incremental.test
index 18df73a95764..bc9a61bae782 100644
--- a/test-data/unit/check-incremental.test
+++ b/test-data/unit/check-incremental.test
@@ -7929,6 +7929,58 @@ from a import b  # type: ignore[attr-defined]
 main:2: error: Unused "type: ignore" comment
 [out2]
 
+[case testConfigWarnUnusedSectionIncremental]
+# flags: --config-file=tmp/mypy.ini
+import m
+[file m.py]
+import a
+[file m.py.2]
+import a  # touch
+[file a.py]
+import foo  # type: ignore
+[file mypy.ini]
+\[mypy]
+warn_unused_configs = true
+\[mypy-bar]
+\[mypy-foo]
+[file mypy.ini.3]
+\[mypy]
+warn_unused_configs = true
+\[mypy-foo]
+[out]
+tmp/mypy.ini: note: unused section(s): [mypy-bar]
+[out2]
+tmp/mypy.ini: note: unused section(s): [mypy-bar]
+[out3]
+
+[case testConfigWarnUnusedSectionIncrementalTOML]
+# flags: --config-file tmp/pyproject.toml
+import m
+[file m.py]
+import a
+[file m.py.2]
+import a  # touch
+[file a.py]
+import foo  # type: ignore
+[file pyproject.toml]
+\[tool.mypy]
+warn_unused_configs = true
+\[[tool.mypy.overrides]]
+module = "bar"
+\[[tool.mypy.overrides]]
+module = "foo"
+warn_unreachable = true
+[file pyproject.toml.3]
+\[tool.mypy]
+warn_unused_configs = true
+\[[tool.mypy.overrides]]
+module = "foo"
+[out]
+tmp/pyproject.toml: note: unused section(s): module = ['bar']
+[out2]
+tmp/pyproject.toml: note: unused section(s): module = ['bar']
+[out3]
+
 [case testAddedMissingModuleSkip]
 # flags: --follow-imports=skip
 import mod
diff --git a/test-data/unit/cmdline.test b/test-data/unit/cmdline.test
index 2b3f48fec4a0..0acba23abea0 100644
--- a/test-data/unit/cmdline.test
+++ b/test-data/unit/cmdline.test
@@ -535,7 +535,6 @@ variable has type "bytes")
 [file mypy.ini]
 \[mypy]
 warn_unused_configs = True
-incremental = False
 \[mypy-bar]
 \[mypy-foo]
 \[mypy-baz.*]
@@ -555,7 +554,7 @@ incremental = False
 [file spam/__init__.py]
 [file spam/eggs.py]
 [out]
-Warning: unused section(s) in mypy.ini: [mypy-bar], [mypy-baz.*], [mypy-emarg.*], [mypy-emarg.hatch], [mypy-a.*.c], [mypy-a.x.b]
+mypy.ini: note: unused section(s): [mypy-bar], [mypy-baz.*], [mypy-emarg.*], [mypy-emarg.hatch], [mypy-a.*.c], [mypy-a.x.b]
 == Return code: 0
 
 [case testPackageRootEmpty]