Steps:

1. flutter create test_app --platforms ios and cd test_app
2. flutter config --enable-swift-package-manager (because majority of my apps use it, or whatever reason)
3. Add config: enable-swift-package-manager: false to pubspec (with proper indentations of course)
4. flutter pub add firebase_core
5. Run flutter pub get. cd ios/
6. Update the first line of Podfile so that the minimum deployment target is "15.0", and uncomment the line (required by Firebase, unrelated to the bug).
7. pod install. Check Podfile.lock, it contains the FirebaseCore (because we get it through Cocoapods)
8. cd ios (or any other directory within the app's directory other than it), run flutter pub get. The config is ignored. Regenerate Podfile from symlinks with pod install. The FirebaseCore was removed from the lock, as it's fetched from SwiftPM now and not Cocoapods 🙃

The lines below sound like they have some knowledge of why it's happening. It should check the manifest of the package closest in the directory tree, not the current directory.

➜  ~ flutter --version
Flutter 3.35.2 • channel stable • https://github.com/flutter/flutter.git
Framework • revision 05db968908 (5 weeks ago) • 2025-08-25 10:21:35 -0700
Engine • hash abb725c9a5211af2a862b83f74b7eaf2652db083 (revision a8bfdfc394) (1 months ago) • 2025-08-22 23:51:12.000Z
Tools • Dart 3.9.0 • DevTools 2.48.0