Lacking knowledge, I couldn't understand much of what is written in Martinis's paper (reference given by Strilanc), not to say to attempt to counter-argue. However, I have the impression that the manner with which quantum tomography is mentioned at two places of the paper is a little bit biased or anyway not very clear. One first reads there:
"In level 1 ... Quantum process tomography is often performed on one- and two-qubit gates, which is important as it proves that proper quantum logic has been achieved. ..."
I suppose that readers of it would afterwards (highly likely) not have any doubts on a similar "importance" of QPT for more-than-two-qubit gates. (I personally think that QPT is extremely important for a really solid proof of correctness of any quantum gate or circuit, but this is of no relevance for the present post of mine.)
Next one reads from the paper:
"In level 2 ... Process tompgraphy can be performed, but is typically abandoned because (i) the number of measurements scales rapidly with increasing number of qubits, (ii) information on error coherence is hard to use and (iii) it is difficult to separate out initialization and measurement errors. ..."
In my view (a) this doesn't (clearly) tell the reader whether for cases of more than 2 qubits quantum process tomography remains important for the proof of "proper quantum logic" just as in the case of one or two qubits, (b) this (in my interpretation) is in fact merely a more detailed formulation of the sentence in Wiki on quantum tomography claiming that QPT is practically infeasible for cases of larger number of qubits and consequently, if the "importance" of (a) is true, then the stuffs of the higher levels treated in the paper would lose their significance.