Yeah, that would be a problem.I couldn't find a set of risers that had the right angle, height, length and diameter to match up to the Yamaha "Y" pipe that go to the transom.
I did the same but with full closed cooling. My manifolds have 50/50 coolant flowing through them all the time. Only heat exchanger discharge raw water going to the risers and then out with the exhaust.I kind of like the idea of the manifolds matching the temperature of the heads though. Maybe less likely to warp them but I'm no mechanical engineer though.