One of the concerns I had with selecting a liner was that if I went with the smaller it would be too small and the larger would have too much excess that would be wasted. My super smart wife suggested that I use visquene to test the sizes to see which is appropriate. I'll be getting the visquene I need this weekend and doing a test with the smaller size (the one I think will work perfectly) to see if I'm correct.
If you cut the dogleg off you would have to rely only on the pond coat as a sealant. Not that it cant I'm just saying it out loud.
I don't want to make up your mind but I think the work to cut out the dogleg will be less than trying to finesse the liner into that space. But then again I'm not there. Good Luck!