Unfortunately fixing this behaviour will mean introducing a potentially breaking change.

We do suggest using a custom method that checks for unity exit/enter playmode events https://docs.unity3d.com/2021.1/Documentation/ScriptReference/EditorApplication-playModeStateChanged.html and have - in this case - set to true. Something like this works and should work for your case:

[CreateAssetMenu]
[InitializeOnLoad]
public class ScriptableObjectSample : ScriptableObject
{
public bool X { get; set; }

void OnEnable()
{
EditorApplication.playModeStateChanged += LogPlayModeState;
Debug.Log("Application.isPlaying " + Application.isPlaying + " - CustomApplicationIsPlaying " + X);

if (X)
{
Debug.Log("This message never displays");
}
}

private void OnDisable()
{
EditorApplication.playModeStateChanged -= LogPlayModeState;
}

void LogPlayModeState(PlayModeStateChange state)
{
Debug.Log("LogPlayModeState " + X);

if (state == PlayModeStateChange.ExitingEditMode)
{
X = true;
}
else if (state == PlayModeStateChange.ExitingPlayMode)
{
X = false;
}
}
}