Hm, do we have any other E6/C6 owners that can confirm that the handshaking issues while using a direct connection have been fixed with the latest FW? I'm skeptical. Unfortunately I haven't my 55E6 anymore to check myself.
Anyways, it's not only the PS4 Pro but also other devices that rely on HDMI 2.0 such as the Xbox One S.
As for the B6 with its different SOC and different FW, AFAIK it had similar problems at the beginning, but a FW update fixed it a couple of months ago already.
I've had maybe 2-3 handshake issues with my PS4 Pro and my E6, but that's it. I haven't had any with the Xbox One S or other 4K devices. Perhaps you had cabling issues.