you seem to have covered all the obvious things already. my crosstrek is eerily smooth most of the time, except when the cvt is cold. my previous '02 legacy made some hideous noises when the lug nuts (all 10 of them!) weren't tightened on the right side, but a tire rotation should have fixed that.
since the problem seems to be readily reproducible (highway speed under load), you could try a few quick experiments, like downshifting, or neutral, at highway speeds, to try to isolate the noise to engine vs transmission, if you haven't done that already. and i presume you've checked for things like warped brake rotors?