Yes, this will use D65 as the illuminant for the CIE XYZ to CIE Lab transformation, (default is currently D50 but will very likely change to D65 in the future).
There is no gamut mapping in Colour (yet), so you are a bit in uncharted territory here and I don’t know how Argyll works under the hood, so I cannot really comment on that. If the output of Argyll is gamut mapped with Relative Colorimetric Rendering Intent, I’m then not surprised at all that you get discrepancies as it involves projecting colours on the gamut boundaries.