Though we all know of boatbuilders who routinely slather just about everything with linseed oil and swear by it, there are also some of us who have read the test results coming from sources like the Forest Products Lab, and avoid putting it on anything. It tends to test poorly as a preventative for weathering and decay, doesn't do well in terms of moisture exclusion and in some cases, it is even sighted as a potential source of "food" for some of the organisms that will eventually destroy the wood and/or canvas. In many cases, you're left with the feeling that it will probably be ineffective at best and possibly even do more harm than good.
In your original plan (add mildewcide to some part of the canvas/paint/filler skin and cover a linseed oil-coated hull with it) you would be attempting to prevent mildew and then placing that directly up against an oiled surface that seems to be a prime area to grow mildew (see exerpt shown below from a FPL publication).
As explained, mildew isn't going to directly harm the wood (or filler or enamel) but it will absolutely eat and deteriorate natural cotton canvas. That's the part of the skin that needs the protection, the canvas itself. Filler doesn't completely saturate the canvas and mildewcide isn't 100% effective, so there will still be plenty of raw canvas fibers present on the inside of the canoe's skin. Add a little water and between the oil, the cotton fibers and moisture, you will have provided a nice little smorgasbord with drinks for the mildew and various other hungry micro-critters - some of which prefer to dine on wood. Throw in some pleasant temperatures and they'll all be happy as clams.
The wood/canvas canoe is a marvelous invention and we have all seen how long they can last and how they can be repaired or restored and made good to go for another century or better. On the other hand, from a boatbuilding perspective, they're a hodge-podge of techniques that essentially doom them from the start (mixtures of materials which expand and contract with others that don't, unbedded raw wood joints, wood that's finished on one side but raw on the other, brass fasteners instead of the stronger and much more durable bronze, etc.) and we have all seen what happens to far too many of these boats when they no longer get proper maintenance and storage. I'm sure that there are plenty of folks who will disagree with me, but I see the use of linseed oil on a wood/canvas canoe as being another of these undesirable building practices. Though it may temporarily make the hull look like you're helping it, that's not likely to last very long and it would seem just as unlikely that it's really helping anything at all. If you take good care of your wood/canvas canoe and treat it as something of value, it should last just fine without linseed oil on anything. If you don't take good care of the boat, the addition of linseed oil isn't likely to make any difference.
