Bug: Indexing fails when using VFS overlays

Description

We recently updated rules_xcodeproj from 1.5.1 to 1.8.1 and started seeing errors in Xcode's background indexer.

The Index Build tasks are ok, but the background indexer (the one when you open/edit files) is failing to find other modules.

We don't use rules_ios, just rules_apple and rules_swift.

I did manage to set up a repro here.

Reproduction steps

Please clone https://github.com/andre-alves/xcodeproj_indexing_error_repro and do these steps:

bazelisk run //BazelSample:BazelSampleXcodeProj
open BazelSample/BazelSample.xcodeproj
Do nothing, just wait for all Index Build tasks to finish.
When BazelSample is Ready, open DrinkDiscoveryInteractor.swift
Check the background indexing logs.

Tested with Xcode 14.3.1 and 14.1

Expected behavior

Expected no error logs in Xcode's background indexer.

rules_xcodeproj version

1.8.1

Xcode version

14.3.1

Bazel version

6.2.1

rules_apple version

2.5.0

rules_swift version

1.9.1

Additional information

No response

Start by cloning the linked xcodeproj_indexing_error_repro repository and running bazelisk run //BazelSample:BazelSampleXcodeProj, then open the generated project and wait for Index Build tasks to finish. Open DrinkDiscoveryInteractor.swift and inspect the background indexing logs under the stated Xcode, Bazel, rules_apple, and rules_swift versions; done means the background indexer reports no errors.