There appears to be a regression in the way collider sizes are calculated when in the prefab the gameobject has a non unit scale. In this case the root gameobject contains a cylinder physics shape, the renderer and has a uniform scale of .5. Below are pictures of the prefab and entity in 1.0.16 and 1.2.1 The issue is also present in 1.2.3 and 1.3.0-exp.1, and also happens with primitives and > 1 scales. Is this a known issue or by design?
It can easily be fixed by moving the renderer to a child gameobject and scaling that, but that results in multiple entities which introduces unnecessary complexity when having to access components on both entities.

same problem with capsule, box and sphere, but they are aligned with the pivot

hull and mesh fail with the following error, I did not spend a lot of time trying to figure out why
.11/Custom Physics Authoring/Unity.Physics.Custom/Utilities/PhysicsShapeExtensions.cs:357)
Unity.Physics.Editor.PhysicsShapeAuthoringEditor+PreviewMeshData.GetInputHash (Unity.Physics.Authoring.PhysicsShapeAuthoring shape, Unity.Collections.NativeList1[T] currentPoints, Unity.Collections.NativeArray1[T] hashedPoints, Unity.Physics.ConvexHullGenerationParameters hashedConvexParameters, Unity.Physics.ConvexHullGenerationParameters& currentConvexProperties) (at Assets/Samples/Unity Physics/1.0.11/Custom Physics Authoring/Unity.Physics.Custom.Editor/Editors/PhysicsShapeAuthoringEditor.cs:254)
Unity.Physics.Editor.PhysicsShapeAuthoringEditor+PreviewMeshData.SchedulePreviewIfChanged (Unity.Physics.Authoring.PhysicsShapeAuthoring shape) (at Assets/Samples/Unity Physics/1.0.11/Custom Physics Authoring/Unity.Physics.Custom.Editor/Editors/PhysicsShapeAuthoringEditor.cs:273)
Unity.Physics.Editor.PhysicsShapeAuthoringEditor.GetPreviewData (Unity.Physics.Authoring.PhysicsShapeAuthoring shape) (at Assets/Samples/Unity Physics/1.0.11/Custom Physics Authoring/Unity.Physics.Custom.Editor/Editors/PhysicsShapeAuthoringEditor.cs:450)
Unity.Physics.Editor.PhysicsShapeAuthoringEditor.OnSceneGUI () (at Assets/Samples/Unity Physics/1.0.11/Custom Physics Authoring/Unity.Physics.Custom.Editor/Editors/PhysicsShapeAuthoringEditor.cs:1106)
(wrapper dynamic-method) System.Object.lambda_method(System.Runtime.CompilerServices.Closure,UnityEditor.Editor)
UnityEditor.SceneView.CallOnSceneGUI () (at <9ebc778a6d634deab4b52bba4afceb9f>:0)
UnityEditor.SceneView.HandleSelectionAndOnSceneGUI () (at <9ebc778a6d634deab4b52bba4afceb9f>:0)
UnityEditor.SceneView.DoOnGUI () (at <9ebc778a6d634deab4b52bba4afceb9f>:0)
UnityEditor.SceneView.OnSceneGUI () (at <9ebc778a6d634deab4b52bba4afceb9f>:0)
UnityEngine.UIElements.IMGUIContainer.DoOnGUI (UnityEngine.Event evt, UnityEngine.Matrix4x4 parentTransform, UnityEngine.Rect clippingRect, System.Boolean isComputingLayout, UnityEngine.Rect layoutSize, System.Action onGUIHandler, System.Boolean canAffectFocus) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.IMGUIContainer.HandleIMGUIEvent (UnityEngine.Event e, UnityEngine.Matrix4x4 worldTransform, UnityEngine.Rect clippingRect, System.Action onGUIHandler, System.Boolean canAffectFocus) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.IMGUIContainer.DoIMGUIRepaint () (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.UIR.RenderChainCommand.ExecuteNonDrawMesh (UnityEngine.UIElements.UIR.DrawParams drawParams, System.Single pixelsPerPoint, System.Exception& immediateException) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
Rethrow as ImmediateModeException
UnityEngine.UIElements.UIR.RenderChain.Render () (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.UIRRepaintUpdater.Update () (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.VisualTreeUpdater.UpdateVisualTreePhase (UnityEngine.UIElements.VisualTreeUpdatePhase phase) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.Panel.UpdateForRepaint () (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.Panel.Repaint (UnityEngine.Event e) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.UIElementsUtility.DoDispatch (UnityEngine.UIElements.BaseVisualElementPanel panel) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.UIElementsUtility.UnityEngine.UIElements.IUIElementsUtility.ProcessEvent (System.Int32 instanceID, System.IntPtr nativeEventPtr, System.Boolean& eventHandled) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.UIEventRegistration.ProcessEvent (System.Int32 instanceID, System.IntPtr nativeEventPtr) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.UIElements.UIEventRegistration+<>c.<.cctor>b__1_2 (System.Int32 i, System.IntPtr ptr) (at <7a9a3b5778c347b6839df652ebdc3172>:0)
UnityEngine.GUIUtility.ProcessEvent (System.Int32 instanceID, System.IntPtr nativeEventPtr, System.Boolean& result) (at <757be09432284cd18660f117f30505e6>:0)