I just picked up a Meridian Explorer 2 to find out if that was true. It some cases it is, in some cases it is not. Several of the "DAC unfolded" versions offered roughly similar performance to the "software unfolded" versions. However, some of them were actually quite different. For the most part, they were the tracks that unfolded all the way to 24/192, which definitely sounded better. But a few of them that only unfolded to 24/96 sounded quite different as well, particularly ELP's "Brain Salad Surgery" (which I also own in 24/96).
Whether or not it sounds better could be considered subjective, and I still feel that the use of exclusive, hardware-based decoding technology is an invitation to be usurped by a more openly adaptable design, but it is different.
Just to be clear, I don't think there's any "magic" going on here, but I'm fairly certain after a bit of listening that the folks who are mastering these MQA tracks are getting some degree of choice as to what is being compressed down into that noise layer. The fortunate part is that some of the folks who are mastering these new MQA versions are talented enough to essentially create what I see as not one but TWO good masters of these recordings, in some cases. Others are just putting their stamp on it with little additional effort. And yet another group seems to be making some positive changes, but not fully utilizing the technology.
So, IMO, you are partially right but not completely. It has everything to do with the master and who is doing the mastering, yes. But it also has to do with their willingness to use the technology and how adept they are with it on these first forays into MQA. In the end, there is no "magic" inherent in the technology - it is all about how skilled and creative the mastering engineers are in using it.