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I have to say, you're comparing two totally different boats there. If it were me, the final look would be less important than the intended usage, assuming you want to fix it up. You probably know this, but even if you're talking a Discovery 164, the Sundowner is going to a faster, more straight lined boat whereas the Discovery will be better in Class I, II rocky rivers (unless you're a downriver racer, but that's a whole different ball of wax).
The patches can definitely be made to blend into the outside of the hull. If well feathered and with a coat of paint on the top they will be difficult to notice. I usually find that patches are easier to see on the inside of the hull. I don't know if it's just because we usually don't take the time to fare them as well, or we don't put a thick coat of paint on the inside like we usually do on the outside.
Many years ago I took a MR Explorer in even worse condition. I got it for free, yes, but it needed much more work. The gunwales were totally rotted and the boat had fallen off the roof of a car going about 45 mph. It was a glass boat (similar to ToughWeave). It has 4 head sized holes - 2 in front of the bow seat and 2 in front of the stern. Plus it had a crack running along the chine about 4 feet long from one of the stern holes. The thing was a mess. I patched the glass, installed Old Town vinyl gunwales (cheap and durable), spray painted it and rebuilt the flotation tanks (yea, they were messed up too). Most of the patching was done in the outside car port of the apartment I lived in at the time. That boat served for several years at the cabin of my Dad's friend in Wabakimi Park in Ontario. Paddled strait and true, never leaked, ran (and swam) class II... it was a great boat. It wintered there for several years protected only by a ridge pole to block falling trees. Jack gave up the cabin several years ago and we brought the canoe back to his house. I'd paddle it and take a trip in it today without hesitation.
To me, the real question is will you get enjoyment out of the rebuild project. For some people, and I put myself in this category, there is nothing like bringing something left for dead back to life. The MR sure was fun to paddle knowing what it had been through and how I brought it back.
Good luck,
John