This isn't great for Layer. I think most companies want to own their chat stack. Its not complex enough, like say Stripe, to need a 3rd party. Has anyone used Layer and felt they added value?

They used Google's database service and Pusher, so only in a limited sense do they "own their chat stack".

Are there any true peer to peer chat apps left, or do they all go through some server now, even after call setup?

I really doubt it. Remember when you could just send someone a file, because their IM client allowed you to connect to each other directly?

I wonder if there's a good way to do this now, as some plug in somewhere... Even XMPP's file forwarding functionality fails for me.

Broadband and wireless routers kinda killed this. It's now typical for every computer on your home network to be behind a NAT, so to enable direct connect, you need to manually punch a hole in your router's firewall. The spyware situation of the early 2000s (which caused Microsoft to bundle a personal firewall with WinXP) didn't help either. Most users are not willing to fiddle with their network connection just so someone on the Internet can directly connect to them.

WebRTC allows for a peer-to-peer data channel and does the heavy lifting of NAT punch through for you. I've mostly been messing with the video chat side of things recently, but would be curious to see if the data channel could be used for large file transfers.

Hardly killed it. There's a reason UPnP exists.

"Are there any true peer to peer chat apps left"

Bittorrent recently released 'Bleep' which supports encrypted peer-to-peer chat including image transfer. It holds the message locally until a direct connection to the receiver is established.