It can mean both. More specifically, the paper uses the term "Heterogeneous ISA", which more often means that the ISAs are completely different (e.g. ARM vs. x86). It does reference previous work in that area, but does not go there itself.

I've noticed that some authors prefer to distinguish the two types of heterogeneous -CPU systems by instead using the term "Partial ISA" when referring to when there is a shared core instruction set.