diff --git a/build-support/bin/check_inits.py b/build-support/bin/check_inits.py
index 9d3a559ee80..5d946f0009e 100755
--- a/build-support/bin/check_inits.py
+++ b/build-support/bin/check_inits.py
@@ -21,11 +21,17 @@ def main() -> None:
     files = itertools.chain.from_iterable(
         [Path().glob(f"{d}/**/__init__.py") for d in DIRS_TO_CHECK]
     )
-    bad_inits = [f for f in files if bool(f.read_text())]
-    if bad_inits:
+    root_init = Path("src/python/pants/__init__.py")
+    if '__import__("pkg_resources").declare_namespace(__name__)' not in root_init.read_text():
+        die(
+            f"{root_init} must have the line "
+            '`__import__("pkg_resources").declare_namespace(__name__)` in it.'
+        )
+    non_empty_inits = [f for f in files if bool(f.read_text()) and f != root_init]
+    if non_empty_inits:
         die(
             "All `__init__.py` file should be empty, but the following had content: "
-            f"{', '.join(str(f) for f in bad_inits)}"
+            f"{', '.join(str(f) for f in non_empty_inits)}"
         )
 
 
diff --git a/src/python/pants/__init__.py b/src/python/pants/__init__.py
index 5284146ebf2..4f581f30081 100644
--- a/src/python/pants/__init__.py
+++ b/src/python/pants/__init__.py
@@ -1 +1,3 @@
+# NB: We need to declare a namespace package because we have the dists `pantsbuild.pants` and
+# `pantsbuild.pants.testutil`, which both have the module `pants`.
 __import__("pkg_resources").declare_namespace(__name__)
diff --git a/src/python/pants/backend/python/goals/setup_py.py b/src/python/pants/backend/python/goals/setup_py.py
index 488107e4e8a..eb4895b3f91 100644
--- a/src/python/pants/backend/python/goals/setup_py.py
+++ b/src/python/pants/backend/python/goals/setup_py.py
@@ -531,13 +531,19 @@ async def generate_chroot(request: SetupPyChrootRequest) -> SetupPyChroot:
     target = exported_target.target
     resolved_setup_kwargs = await Get(SetupKwargs, ExportedTarget, exported_target)
     setup_kwargs = resolved_setup_kwargs.kwargs.copy()
+    # NB: We are careful to not overwrite these values, but we also don't expect them to have been
+    # set. The user must have have gone out of their way to use a `SetupKwargs` plugin, and to have
+    # specified `SetupKwargs(_allow_banned_keys=True)`.
     setup_kwargs.update(
         {
-            "package_dir": {"": CHROOT_SOURCE_ROOT},
-            "packages": sources.packages,
-            "namespace_packages": sources.namespace_packages,
-            "package_data": dict(sources.package_data),
-            "install_requires": tuple(requirements),
+            "package_dir": {"": CHROOT_SOURCE_ROOT, **setup_kwargs.get("package_dir", {})},
+            "packages": (*sources.packages, *(setup_kwargs.get("packages", []))),
+            "namespace_packages": (
+                *sources.namespace_packages,
+                *setup_kwargs.get("namespace_packages", []),
+            ),
+            "package_data": {**dict(sources.package_data), **setup_kwargs.get("package_data", {})},
+            "install_requires": (*requirements, *setup_kwargs.get("install_requires", [])),
         }
     )
     key_to_binary_spec = exported_target.provides.binaries