Update bazel incompatible flag list (#4891)

Note one of these was added in 8.0.1, so this PR requires #4888. I just
forgot to check flags when updating, and figured it's just as well to
split this.

- `--incompatible_disable_native_apple_binary_rule`: Not sure why I
didn't have this before, maybe a copy-paste error? It's not new, it's
documented as deprecated... but even though it should be a no-op,
bazelisk recommends adding it.
- `--incompatible_disallow_empty_glob`: #4783 removed the conflict; I
mistakenly removed the comment instead of uncommenting
- `--incompatible_locations_prefers_executable`: New flag;
https://github.com/bazelbuild/bazel/releases/tag/8.0.1

Author: jonmeow

.bazelrc

@@ -166,10 +166,12 @@ common --incompatible_default_to_explicit_init_py
 common --incompatible_depset_for_java_output_source_jars
 common --incompatible_depset_for_libraries_to_link_getter
 common --incompatible_disable_native_android_rules
+common --incompatible_disable_native_apple_binary_rule
 common --incompatible_disable_native_repo_rules
 common --incompatible_disable_objc_library_transition
 common --incompatible_disable_target_provider_fields
 common --incompatible_disallow_ctx_resolve_tools
+common --incompatible_disallow_empty_glob
 common --incompatible_disallow_legacy_py_provider
 common --incompatible_disallow_sdk_frameworks_attributes
 common --incompatible_disallow_struct_provider_syntax
@@ -185,6 +187,7 @@ common --incompatible_fail_on_unknown_attributes
 common --incompatible_fix_package_group_reporoot_syntax
 common --incompatible_java_common_parameters
 common --incompatible_legacy_local_fallback
+common --incompatible_locations_prefers_executable
 common --incompatible_make_thinlto_command_lines_standalone
 common --incompatible_merge_fixed_and_default_shell_env
 common --incompatible_merge_genfiles_directory