ID-Properties as well as bpy.types properties show up in the Custom Properties panel, although they are separated from Python perspective (they aren't internally).

If you add a bpy.types property...

bpy.types.Object.prop = bpy.props.StringProperty()
bpy.context.object.prop = "foobar"

it will show in the Custom Properties panel, and you can change it there (even to 123 or [1,2,3], it will be interpreted as string).

But if you click the Edit button and type e.g. 123 into the popup's value field and confirm, the property (bpy.context.object.prop) will be cleared and disappear from panel (there's no ID property with this name either).

If the property is a bpy.types property, there shouldn't be type casting, and it would avoid losing this property.

There's another issue if you use .prop as property name:
Try to add an ID property in the panel by clicking Add - it will try to create a property with the default name prop (+number if needed). But as there's a bpy.types property with that name, it seems to name-conflict and is removed immediately.
I guess it should check for bpy.types properties and use a name not already in use?