I use the steam overlay with Sins sometimes. Stardock doesn't have any obligation to make it work with the steam overlay, and if it doesn't work, so what?
Anyways you have a 95% chance of it working with elemental, other stardock games do.
EDIT: I forgot to mention this but I do think Impulse is getting an instant messaging system in it's next big update, which I think is going to be at the same time the Elemental beta starts. So you could just use that, assuming it also comes with an overlay