Unfortunately, setting the layout breakpoints under Site Settings using em units is not currently an available feature. This would be considered a feature request, and I’m tagging your inquiry as such for our developers so that it can be considered for a future release.
In the meantime, you can use custom code to add media queries using em units. We also invite you to post this feature request on our Github account. Please note that this is not an official support channel but a respective member of the development team will respond to your post as soon as they are available. Please follow this guide which outlines the steps required to post on our Github: https://github.com/elementor/elementor/blob/master/.github/CONTRIBUTING.md.