Your understanding is basically correct. The first create cell is indeed encrypted with 1 layer, the second 2 layers, the third 3 layers, etc.
However, Tor takes a different approach when encrypting the second create cell. The second create cell is first encrypted with the public key of Relay 2, and next encrypted with the session key of Relay 1.
It looks ...
these matters are totally unrelated: Tor is a Network layer, sort of speaking, and - HDD security - is a server-layer or service-layer, regardless of the network the Server is exposed to: Internet/Clearnet, Tor, I2P e.t.c..