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The poly paint will provide a decent barrier coat, but that really isn't the issue with a boat that is not always in the water anyway.
You can apply gel coat, but it will not cure to a nice finish like the paints will. So it's much more labor intensive to get a decent finish, and it is fibreglass resin, primarily, and is not impermeable to water. (again, not a huge issue on a canoe that is out of the water more than in it.) Fiberglass is permeable to water at a microscopic level, it's not going to "leak" without paint unless the repairs are faulty.
One part poly paint will likely do a decent job for you but will not withstand abuse, bumps and scrapes as well as the two-parts will. They are a lot less expensive, though, and may serve your purpose.
I would think that one part poly would be no more money than gelcoat.