Something caught my attention of what Brad Myers wrote in this 2001 paper on the history of human-computer interaction technologies:
Alan Kay proposed the idea of overlapping windows in his 1969 doctoral thesis, and overlapping windows first appeared in 1974 in his Smalltalk system at Xerox PARC, and soon afterward in the InterLisp system.
So, after Smalltalk, Interlisp was the second system with overlapping windows. The Interlisp environment Myers refers to is not Interlisp-D though but the one described here: