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I don't think this is a question of water running "uphill" anyway, since the entire platform that the muffler rests on is below the waterline.water can run uphill, via capillary action. That's how trees get water from their roots... and it can go a long, long way uphill.
NK, I'm very curious too. Our boat is virtually identical to yours, i.e. same rudder/skeg/aperture, exact same platform over the stuffing box, etc (but our waterlift muffler is mounted elsewhere).
I have always assumed that the area under the platform was filled with chop and resin, and that the shaft tube ran through this "solid" area. But practically speaking, I'm not certain that it could be completely solid. There could easily be some small hairline voids through which water under pressure could pass. The source would most likely be a bad seal where the shaft tube exits the boat in the aperture, with vibration/cavitation from the spinning prop exacerbating it and allowing some ingress.
Normally I would advise haul the boat and sort it out. But if I was in your shoes, having had some budget busting repairs already this season, I would probably hold off until next winter haul-out. (This assumes you are not planning another long voyage this year?) Keep a close eye on it, maybe see if you can stop the leak by sealing the pinhole. You might also try diving and sealing around the shaft tube with a sealant that can cure underwater.