Glad to hear you were inspired by one of our videos
The flexible substrate Sherman used in the video is PET or Polyethylene terephthalate. it’s a good choice for flex substrates but certainly isn’t the only one. Here at Voltera we also like to use kapton (a type of Polyimide film) for flex work.
In terms of sourcing it you can find it just about anywhere, I think we get most of ours from https://www.mcmaster.com/
In terms of where you place the magnets you don’t need to worry to much. We’ve got a setting in the beta tab of the software that lets you set your minimum raise height. There’s a video illustrating how it works here.
As far as the solutions you’ve already used for vias I quite like them. I’ve not actually tried running a wire through a board myself but I’ve definitely done a few boards where I’ve just filled holes with ink rather than using rivets. I find there are benefits to both methods, if I’ve got a through-hole component I definitely want to go with a rivet though. I think your approach to solving the problem based on the intended use of the board is really the right way to go about things.