Tim --
Working again from a dim memory of what I did about 40 years ago, I am pretty sure that when I built a Trailcraft eons ago, I used nothing like a bedding compound, and had no problems with leakage at the canvas seams at the stem. Neither did I have any of the sort of bleeding through the canvas that shows in your picture, and I only painted the canvas on the Trailcraft, no filler. I think that the bleeding in your picture is the result of old paint that had at least a few small cracks in it. When I painted the Trailcraft canvas, I did use what was then a relatively new product that I got from Sears -- a 2 part epoxy paint, and I think I put two coats on. I seem to remember that the paint soaked well into the canvas, to the point that the color showed through on the inside, visible between the stringers. If I were painting a SOF boat now, I think I would use 2-3 coats of an oil-based paint (I'm not sure the epoxy paint did any better than ordinary paint), which I suspect would soak into the canvas better than a water-based paint. And if I needed something like a bedding compound but wanted it fast, I think I would try a paintable caulking compound; there are usually at least a couple of paintable caulks in tubes available in Lowe's or Home Depot. Like the others have said, stay away from applying silicone anywhere near where you might want to paint.
I suspect that the canvas on a SOF canoe or boat flexes far too much at times for a traditional filler to be effectively used. I may well be wrong, buat my impression is that, while fillers have some degree of flexibility, they are intended to be used on canvas backed by planking, and are not intended to be flexed as much as the skin of a SOF boat will be.
Greg