In depth TOR encryption details

I am currently struggling with understanding the details of a connection in tor, mainly because I try to understand PCTCP. In this paper the authors claim that the changes are local to the onion router which is using PCTCP and that IPSec completely replaces TLS in the sense of the security goals integrity, confidentiality and authenticity.

Fine. I understood the basic onion routing principle, I understood Tor (I guess) and I understood the intention in PCTCP, but when replacing TLS with IPSec, imho the changes can NOT be local to the onion router using PCTCP unless I have a wrong understanding of the TOR security architecture.

Tor uses onion routing, meaning onion proxy (OP) has negotiated three symmetric keys (K1-3) with each of the onion routers (OR1-3) on the circuit with the Diffie-Hellman key exchange. This are the keys for the "onion skins" which are wrapped off the data flowing down the circuit by the onion proxies. (I see no possibility to introduce IPSec here)

But is this the only encryption in TOR, or are the connections between the onion routers encrypted too? (TLS, would be replacable by IPSec) If so, why is this necessary?

Further PCTCP states that to avoid an adversary to count the connections IPSec will be introduced. But the threadmodel defined in TOR assumes that an adverary can run its own onion router, with which he could count the connection even with IPSec enabled.