Today (literally, today), the Supreme Court took a first shot at narrowing the third party doctrine with respect to hotel room records in Los Angeles. [2] The ruling was largely about the procedure a hotel may use to quash (ask a court to reject) the subpoena, but it shows a willingness to cut back on the third party doctrine. The GPS tracker case also had some commentary suggesting a limit to the third party doctrine, but it was ultimately decided based on the physical intrusion of the device.
[1] Alternet's very negative take on the issue: http://www.alternet.org/8-ways-police-can-spy-you-without-wa...
[2] http://www.politico.com/story/2015/06/hotel-guest-list-priva...
The hotel case you mentioned doesn't seem to involve that; in this case, the hotel is opposing the request, so there's an adversarial posture between the third-party data holder and the government over handing over the data.
https://en.wikipedia.org/wiki/Pen_register#Pen_Register_Act
So it's reasonable to speak of the third party doctrine being applied to compelled data disclosures, not just voluntary ones.