In what sense are silicon PUFs unclonable?
The answer lies in "complexity", but I do not believe they are unclonable in the explicit sense, but I can think of ways to get data out depending on how they are made.  It is easy for me to see "ROM" type gates under a SEM, and what PUFs buy you is that the structure is uniform but then you do not know the electrical characteristics.  

In a PUF array, you give it some electrical input and you get a seemingly random, but repeatable output due to [PVT] (Process Voltage Temperature) of the devices 1. You could actually consider this just a huge lookup table of complexity of bit-width and clock depth.  A 32-bit number gives you a 32-bit number out at some clock of X.  The input is generally easily to get to, but the output is buried in the layout.  The output could completely be probed, but you would get an answer for a single input.  (on the reverse engineering side, I could make things current mode so I could not probe them because probing them would cause errors).  Now assume that you have a PUF array that takes a single clock and has a 32-bit output due to a single 32-bit input, that means you'd need a single 32-bit value in your ROM to emulate the PUF.  Otherwise, you need an entry for each clock and input vector.  If you have 32-bits of possible input, for one clock, you'll need $2^{32}$ entries in your rom, and it gets huge from there.

So, (1) If you a voltage mode circuit on the output, (2) have a single entry to map, and (3) have a semiconductor lab, there's no reason you could not get a single output and replace it with the ROM.