Despite being in the Store for more than a year, WhatsApp’s Desktop app still does not support native Windows 10 Notifications.
It appears this is about to change, however, as WBI reports that, starting today, WhatsApp is testing native Windows 10 notifications with Windows 10 Insiders in the Slow, Fast and Skip Ahead rings.
This means WhatsApp notifications now show up in the Action Centre and can be managed using the tools there, including being controllable by the Action Centre Focus feature.
At present, the feature appears to only work while the WhatsApp app is open in the background and is not reliable. Hopefully, at some point, this issue can also be addressed.
If you want to download WhatsApp for Windows, you can get it from this link.