Nova and other third party launchers don't have the correct API access for chrome shortcuts to work, regardless of if you set nova as default.
As you correctly state, your google launcher gets the shortcut, whilst other launchers like nova and others don't.
Its a well known issue with chrome.
Here is the explanation from a comment on the same issue:
The com.android.launcher.action.INSTALL_SHORTCUT broadcast no longer has any effect on your app, because it is now a private, implicit broadcast.
Instead, you should create an app shortcut by using the requestPinShortcut() method from the ShortcutManager class.
https://developer.android.com/preview/behavior-changes.html
Looks for me like an API change at the app developer side. This would mean that the launcher cannot do anything to fix this issue, the apps must use a different API.