It should just work without you needing to do anything else. If it doesn't work, please file an issue following all the guidelines.
Ok I've come to find out the issue is when trying to open the x64 export with bundled assets and only when you are exporting both 32 and 64 bit versions. This seems to be an error with any project I've tried (including Scirra provided demo projects).
Reproduction is simple...
1. Open any demo game provided by Scirra.
2. Export the project for Windows (WebView2) select select "Bundle Assets", "32-bit (x86)" and "64-bit (x64)". Other options don't matter.
3. Launch the exported 64 bit version.
It opens a window with app.localhost/index.html in the title bar but then just says "file not found".
So unless I'm missing something this clearly seems like a bug.