The message is only a recommendation, so it is possible to create custom tables in global scope. It depends on the use case if it's best practice or not.

What do you mean by 'my table is not showing as application scope in the left side filter pane'? For one: you created the table in the global scope, so it's not in an application scope and second, do you mean the navigation pane? For it to show up there, you will need to create a module for it yourself. This is not automatically done.