Well, synthetic Shepard is already a flagrant example of transhumanism. Even the Catalyst says the Commander would die if they chose to destroy the Reapers because the only reason Shepard was alive was thanks to their synthetic implants. They were more machine than organic.
So yeah, let's have further transhumanism in the next ME installment, but preferably something that surprises us, something that goes beyond Robocop.
Actually, no it doesn't. "Even you are partly synthetic" does not necessarily equate to "You will be destroyed as a synthetic".
It is easily a warning about harm, not a claim about death. A slanted statement, but it does not claim Shepard is fully synthetic, fully subject to Destroy.
It just means 'You may or may not die', where Control is 'You'll die but become something' and Synthesis is 'You'll be added to everyone', from its perspective.
IMO Shepard indeed is transhuman by today's standards, in the real world. However, the game itself, via EDI, clarifies (though many don't seem to get this) that the definition of transhuman in the Mass Effect setting is (shifted to) more like augmentations of the brain and/or the mind's workings. It shouldn't be a surprise if a society with augmentations wish to push the transhuman can down the road, seeing as we already seem to be deciding, day to day, that people with hearing implants and artificial limbs or organs, are not exactly 'transhumans'. That brings up transhuman possibly being often a more philosophical stance than a concrete one.