I agree exactly.
The opposing argument is that, in this instance, you are not correcting the EQ for the source. In other words the source "signal" coming from your audio file/player software is fine. The EQ you're compensating for is at the end of the chain, that is, your headphone/speakers. This is why Sonarworks should generally be at the end of the DSP chain before the headphone/speakers.
However, the exception is any room/surround emulation effects. These should do the end processing. Whatever, the theoretical principles, Syliano is right. Putting Sonarworks after surround software yields "weird results."