Custom Visual, when I add table binding, the custom formatting disappears.

I can't help with the majority of what you're asking, but regarding your question about metadata.objects not always being present - in my experience, this is only populated if a property is different to its default value, i.e. modified by the end-user. If your visual has not have any properties modified from the defaults then this will be empty.

The framework will assume the default values (typically specified in your settings.ts) if this is not present for any objects defined. The following code in your post is handling that part:

const settings: VisualSettings = this.visualSettings || 
                                         VisualSettings.getDefault() as VisualSettings;