diff --git a/.bazelrc b/.bazelrc
index dcb73e90697..af3769c38ff 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -1,5 +1,9 @@
 common --enable_platform_specific_config --experimental_enable_bzlmod
 
+# when using repo standalone, we want still to unlock loading the internal repository module
+# actually using things from that module will obviously end up in an error
+common --override_module=codeql_internal=%workspace%/misc/bazel/codeql_internal_stub
+
 build --repo_env=CC=clang --repo_env=CXX=clang++
 
 build:linux --cxxopt=-std=c++20
diff --git a/MODULE.bazel b/MODULE.bazel
index dd8021dcfb0..02cd6a8baa4 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -3,6 +3,8 @@ module(
     version = "0.0",
 )
 
+# this points to our internal repository when `codeql` is checked out as a submodule thereof
+# when building things from `codeql` independently this is stubbed out in `.bazelrc`
 bazel_dep(name = "codeql_internal", version = "0.0")
 local_path_override(
     module_name = "codeql_internal",
diff --git a/misc/bazel/cmake/cmake.bzl b/misc/bazel/cmake/cmake.bzl
index cba271dc517..7d50c7fcdee 100644
--- a/misc/bazel/cmake/cmake.bzl
+++ b/misc/bazel/cmake/cmake.bzl
@@ -22,7 +22,9 @@ CmakeInfo = provider(
 )
 
 def _cmake_name(label):
-    ret = ("%s_%s_%s" % (label.workspace_name, label.package, label.name)).replace("/", "_")
+    # strip away the bzlmod module version for now
+    workspace_name, _, _ = label.workspace_name.partition("~")
+    ret = ("%s_%s_%s" % (workspace_name, label.package, label.name)).replace("/", "_")
     internal_transition_suffix = "_INTERNAL_TRANSITION"
     if ret.endswith(internal_transition_suffix):
         ret = ret[:-len(internal_transition_suffix)]
@@ -120,7 +122,6 @@ def _cmake_aspect_impl(target, ctx):
                 prefix,  # source
                 "${BAZEL_EXEC_ROOT}/%s/%s" % (ctx.var["BINDIR"], prefix),  # generated
             ]
-
     deps = [dep[CmakeInfo] for dep in deps if CmakeInfo in dep]
 
     # by the book this should be done with depsets, but so far the performance implication is negligible
diff --git a/misc/bazel/cmake/setup.cmake b/misc/bazel/cmake/setup.cmake
index 79314d76f85..439bfbb59d7 100644
--- a/misc/bazel/cmake/setup.cmake
+++ b/misc/bazel/cmake/setup.cmake
@@ -19,8 +19,7 @@ endmacro()
 bazel(info workspace OUTPUT_VARIABLE BAZEL_WORKSPACE)
 
 bazel(info output_base OUTPUT_VARIABLE BAZEL_OUTPUT_BASE)
-string(REPLACE "-" "_" BAZEL_EXEC_ROOT ${PROJECT_NAME})
-set(BAZEL_EXEC_ROOT ${BAZEL_OUTPUT_BASE}/execroot/${BAZEL_EXEC_ROOT})
+set(BAZEL_EXEC_ROOT ${BAZEL_OUTPUT_BASE}/execroot/_main)
 
 macro(include_generated BAZEL_TARGET)
     bazel(build ${BAZEL_TARGET})
diff --git a/misc/bazel/codeql_internal_stub/MODULE.bazel b/misc/bazel/codeql_internal_stub/MODULE.bazel
new file mode 100644
index 00000000000..412f621a5ae
--- /dev/null
+++ b/misc/bazel/codeql_internal_stub/MODULE.bazel
@@ -0,0 +1,4 @@
+module(
+    name = "codeql_internal",
+    version = "0.0",
+)
diff --git a/misc/bazel/codeql_internal_stub/WORKSPACE.bazel b/misc/bazel/codeql_internal_stub/WORKSPACE.bazel
new file mode 100644
index 00000000000..e69de29bb2d