Seeing as you’re looking to possible get a WC spot, I’d suggest racing to your strength and minimizing your weaknesses.
Firstly, swimming is swimming at both locations. Both races are in fresh water, and both likely wetsuit swims. Since your swim is sucky (to quote you not me!), it doesn’t make a difference which race you enter, it’s gonna be sucky at either. The freshwater swims aren’t usually effected by adverse weather such as high winds, etc., so again, either venue doesn’t make a difference. If anything, maybe look at the swim course layout for each. The Calgary swim can be in shallow water as the level can drop in the summer months and can be a bit tighter due to the size of the lake and an irregular layout. The Muskoka swim course is more open as there’s lots more room so lesser chance of congestion, and the course has a more straight forward layout. In saying that, I don’t know if either event this year are doing rolling, wave, or mass starts.
Secondly, your strong suit is running. Calgary is pretty much flat around the lake, Muskoka is hilly. Pick your poison; are you a fast and flat runner, or a strength and hill runner. The run is likely where you’ll make up the most ground so figure out which plays to your strength more.
Thirdly, the bike is where you’ll make or break your race. You appear to have some steady times and training in the bag, so your choice of course will play a big factor. Calgary is a more steady, with a long and gradual climb to the highest point on the course which is at the midway mark, then a long gradual downhill to T2. Muskoka is the queen of tough bike courses, lots of ups and downs. It can be a leg destroyer if you’re not a strong biker. The elevation gain for Calgary is in the region of 600 m, Muskoka is 1265 m, it’s definitely a strong riders race.
So in the end, I think for your goals Calgary is the better choice. The Muskoka run will knock the wind out of the strong bikers, so you stand a good chance of making up lost ground there, but the bike will likely take the wind out of your run ability. I think the Calgary bike course is more in line with you as a biker, leaving you with better legs for a fast run. Calgary is not as scenic as Muskoka but who looks at that during a race! And in the end, both venues will have ample lifeguards so there’s no fear of sinking at either venue.
Good luck with whichever one you pick!