Reproduction steps:
1. Create a new Mixed Reality template project
2. Observe the Console

Actual result: “ScriptableSingleton Unity.XR.CompositionLayers.CompositionLayersPreferences already exists” and “ScriptableSingleton Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings already exists” warnings are thrown
Expected result: No errors or warnings are thrown

Reproducible with: 6000.4.0a4
Not reproducible with: 6000.0.62f1, 6000.2.11f1, 6000.3.0b9, 6000.4.0a3

Reproduced on: Windows 11, macOS Sequoia 15.4 (M4)

Note: Full warnings:
{code:java}
ScriptableSingleton Unity.XR.CompositionLayers.CompositionLayersPreferences already exists. This can happen if there are two copies of the asset or if you query the singleton in a constructor.
UnityEngine.Debug:LogWarning (object,UnityEngine.Object)
Unity.XR.CoreUtils.XRLoggingUtils:LogWarning (string,UnityEngine.Object) (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/XRLoggingUtils.cs:45)
Unity.XR.CoreUtils.ScriptableSettingsBase`1<Unity.XR.CompositionLayers.CompositionLayersPreferences>:.ctor () (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/ScriptableSettingsBase.cs:174)
Unity.XR.CoreUtils.Editor.EditorScriptableSettings`1<Unity.XR.CompositionLayers.CompositionLayersPreferences>:.ctor ()
Unity.XR.CompositionLayers.CompositionLayersPreferences:.ctor () (at ./Library/PackageCache/com.unity.xr.compositionlayers@08f04b171ba1/Editor/CompositionLayersPreferences.cs:33) {code}
{code:java}
ScriptableSingleton Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings already exists. This can happen if there are two copies of the asset or if you query the singleton in a constructor. UnityEngine.Debug:LogWarning (object,UnityEngine.Object) Unity.XR.CoreUtils.XRLoggingUtils:LogWarning (string,UnityEngine.Object) (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/XRLoggingUtils.cs:45) Unity.XR.CoreUtils.ScriptableSettingsBase`1<Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings>:.ctor () (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/ScriptableSettingsBase.cs:174) Unity.XR.CoreUtils.ScriptableSettings`1<Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings>:.ctor () Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings:.ctor () (at ./Library/PackageCache/com.unity.xr.compositionlayers@08f04b171ba1/Runtime/CompositionLayersRuntimeSettings.cs:142)
{code}
{code:java}
ScriptableSingleton Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings already exists. This can happen if there are two copies of the asset or if you query the singleton in a constructor. UnityEngine.Debug:LogWarning (object,UnityEngine.Object) Unity.XR.CoreUtils.XRLoggingUtils:LogWarning (string,UnityEngine.Object) (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/XRLoggingUtils.cs:45) Unity.XR.CoreUtils.ScriptableSettingsBase`1<Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings>:.ctor () (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/ScriptableSettingsBase.cs:174) Unity.XR.CoreUtils.ScriptableSettings`1<Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings>:.ctor () Unity.XR.CompositionLayers.CompositionLayersRuntimeSettings:.ctor () (at ./Library/PackageCache/com.unity.xr.compositionlayers@08f04b171ba1/Runtime/CompositionLayersRuntimeSettings.cs:142) UnityEditor.AssetDatabase:LoadAssetAtPath (string,System.Type) Unity.GraphToolkit.Editor.GraphObjectFactory:LoadGraphObjectAtPath (string,System.Type,bool) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/Model/GraphObjectFactory.cs:357) Unity.GraphToolkit.Editor.GraphObject:LoadGraphObjectAtPath (string,System.Type) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/Model/GraphObject.cs:191) Unity.GraphToolkit.Editor.WindowAssetPostprocessingWatcher:DoUpdatesOnAssetRename (string[]) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/UI/Windows/WindowAssetPostprocessingWatcher.cs:37) Unity.GraphToolkit.Editor.WindowAssetPostprocessingWatcher:OnPostprocessAllAssets (string[],string[],string[],string[],bool) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/UI/Windows/WindowAssetPostprocessingWatcher.cs:15) UnityEditor.AssetPostprocessingInternal:PostprocessAllAssets (string[],string[],string[],string[],string[],bool) (at /Users/bokken/build/output/unity/unity/Editor/Mono/AssetPostprocessor.cs:395)
{code}
{code:java}
ScriptableSingleton Unity.XR.CompositionLayers.CompositionLayersPreferences already exists. This can happen if there are two copies of the asset or if you query the singleton in a constructor. UnityEngine.Debug:LogWarning (object,UnityEngine.Object) Unity.XR.CoreUtils.XRLoggingUtils:LogWarning (string,UnityEngine.Object) (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/XRLoggingUtils.cs:45) Unity.XR.CoreUtils.ScriptableSettingsBase`1<Unity.XR.CompositionLayers.CompositionLayersPreferences>:.ctor () (at ./Library/PackageCache/com.unity.xr.core-utils@f0450cbac8d6/Runtime/ScriptableSettingsBase.cs:174) Unity.XR.CoreUtils.Editor.EditorScriptableSettings`1<Unity.XR.CompositionLayers.CompositionLayersPreferences>:.ctor () Unity.XR.CompositionLayers.CompositionLayersPreferences:.ctor () (at ./Library/PackageCache/com.unity.xr.compositionlayers@08f04b171ba1/Editor/CompositionLayersPreferences.cs:33) UnityEditor.AssetDatabase:LoadAssetAtPath (string,System.Type) Unity.GraphToolkit.Editor.GraphObjectFactory:LoadGraphObjectAtPath (string,System.Type,bool) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/Model/GraphObjectFactory.cs:357) Unity.GraphToolkit.Editor.GraphObject:LoadGraphObjectAtPath (string,System.Type) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/Model/GraphObject.cs:191) Unity.GraphToolkit.Editor.WindowAssetPostprocessingWatcher:DoUpdatesOnAssetRename (string[]) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/UI/Windows/WindowAssetPostprocessingWatcher.cs:37) Unity.GraphToolkit.Editor.WindowAssetPostprocessingWatcher:OnPostprocessAllAssets (string[],string[],string[],string[],bool) (at /Users/bokken/build/output/unity/unity/Modules/GraphToolkitEditor/GraphToolkitEditor/UI/Windows/WindowAssetPostprocessingWatcher.cs:15) UnityEditor.AssetPostprocessingInternal:PostprocessAllAssets (string[],string[],string[],string[],string[],bool) (at /Users/bokken/build/output/unity/unity/Editor/Mono/AssetPostprocessor.cs:395)

{code}