I forgot to get back to you. Two days later is better than never I guess.

There’s hidden settings in Factorio if you hold down ctrl+alt while clicking the settings button in the menu. There will be a box called “The Rest” which contains more settings. One of these is for non-blocking saves on Linux/Mac at least. It allows your game to save without freezing. I have no idea if it works on the Switch or how you’d get to it without a keyboard, but I think there’s a way. I know it doesn’t work on Windows, but no one ever mentions the Switch, only that it work on Linux and Mac and not Windows.