OK, here's the scoop. This isn't to do with delay compensation, the phasing you're hearing (it seems to manifest as a loss in high frequencies) is due to the oversampling that's done within Etch. We automatically oversample at 2x internally but this isn't 100% phase linear. If you hunt about for other plugins that do oversampling you'll find exactly the same problem.
We *could* put in an option to do 1x oversampling which would solve the problem, but could you not achieve the same parallel processing using one Pro Tools channel and the wet/dry knob set to 50% in Etch? That way you could still benefit from the oversampling without the phasing issue.