Currently there is no such View Customizer available in SharePoint Framework.
As you already know, currently you can only use JSON formatting to customize your view in SharePoint Online.
SharePoint Framework roadmap.
Overview of the SharePoint Framework.
I cannot reproduce your issue.
Here are my steps:
In the Filters pane, select relevant column value, and save view with a new view name.
Then edit current view:
The Filter section display as below, when I cancel to edit the view, the custom view work as well.
You can check if the list view is your newly created view after cancel to edit the list view.