Since it's just HTML/JS like in regular browser apps, Userflow works perfectly for Electron apps. The only thing that was missing, was the ability to preview flows in draft mode and use the element selector tool.
When previewing flows, there's a new App type dropdown. It defaults to Browser app, which lets you enter the URL of an app running in a browser. Switch to Electron app to preview in an app running locally on your own machine.
It just works!
Here's a real-life example of the design documentation tool, ION, using Userflow in their Electron app: