To be honest, this comment more reflects the reviewer's bias and ignorance, and might be based on some experience from many years ago.
First of all, you can do plane-wave calculations in QuantumATK and the results are just as accurate as in any other code. Now, you cannot do transport simulations with planewaves but for a huge amount of cases where we have benchmarked the LCAO basis sets, the results are very close to planewave. Also, we are confident that the HSE implementation in QuantumATK is actually more accurate than in some other codes.