It would be nice to make all my rise right out of the muffler. I thought about running it in the locker but I'd prefer not to put that big hose in the locker (it's about 3" O.D.) just below the lid. It narrows the opening down too much(my last boat had that arrangement and compromised the locker substantially).
Plus I have 2 CNG tanks in the aft end of the locker that complicate the hose being there.
But it is an option if I have problems (thanks for the idea).
I should be ok according to what I've read and seen on other boats. The larger hose and muffler should take care of any back pressure problems and I calculate the hose and muffler capacity should be safely below the top of the riser unless you pumped it solid with water(not likely). If that happens, the hose in the cockpit locker will flood the engine as well.
The old jacketed pipe system was an elegant solution to most of these problems but I can't turn back now. And I can't imagine what it would cost to duplicate.