Bug: CLI API for indexbuild doesn't pick up flags

Description

When using CLI API to build with indexbuild config, the flags for indexbuild defined in .bazelrc with build:rules_xcodeproj_indexbuild are not applied as expected.

Reproduction steps

1. Apply the following diff

diff --git a/examples/integration/.bazelrc b/examples/integration/.bazelrc
index 45aa71ea..29a8135b 100644
--- a/examples/integration/.bazelrc
+++ b/examples/integration/.bazelrc
@@ -11,6 +11,7 @@ build:rules_xcodeproj --@rules_xcodeproj//xcodeproj:extra_indexbuild_flags='--no
 build:rules_xcodeproj --@rules_xcodeproj//xcodeproj:extra_swiftuipreviews_flags='--noverbose_failures'
 
 build:rules_xcodeproj_integration --define=foo=bar
+build:rules_xcodeproj_indexbuild --define=foo=foo
 
 # Required for sharing cache between Intel and Apple silicon
 build:rules_xcodeproj --@build_bazel_rules_swift//swift:universal_tools

2. cd examples/integration; bazelisk run //:xcodeproj-incremental-bazel-sim_arm64
3. bazelisk run //:xcodeproj-incremental-bazel-sim_arm64 -- --config=indexbuild --generator_output_groups=all_targets "build --announce_rc"
4. Inspect the log

Expected behavior

--define=foo=foo is in the log and applied to build

Actual behavior
INFO: Found applicable config definition build:rules_xcodeproj_integration in file /Users/ycho/Dev/rules_xcodeproj/examples/integration/.bazelrc: --define=foo=bar

rules_xcodeproj version

44b6f046d95b84933c1149fbf7f9d81fd4e32020

Xcode version

15.0

Bazel version

7.1.1

rules_apple version

No response

rules_swift version

No response

Additional information

No response

Start by reproducing the two bazelisk commands from examples/integration and inspect the related entries in examples/integration/.bazelrc, especially the build:rules_xcodeproj_integration and build:rules_xcodeproj_indexbuild configs. Trace how the CLI API selects the indexbuild configuration; done means the indexbuild --define=foo=foo flag appears in the log and is applied to the build.