Teams will snipe any incoming Skype for Business IMs that you receive before you can accept the toast on your real Lync client, which is always fun...

It's either got the Skype for Business Web SDK or raw UCWA jammed in there to log you into Skype, deal with presence, and handle messaging.

Teams is built on top of Skype for Business/Lync, Groups and OneDrive for Business. Under the hood they're the same platform I'd expect that as Teams matures the ability to interoperate will improve