'but it does not solve of the problem of clickjacking.'

I am sorry I don't understand why Intersection Observer V2 doesn't solve the problem of clickjacking.

'So is there a way to detecting if there an element or iframe overlaid on top of my iframe from within my iframe?'

Isn't Intersection Observer V2 supposed to give you that if you don't specify the root element in the Observer options? It is supposed to default to the top-level browsing context’s document node if set as null.