Since https://www.reddit.com/r/linux/comments/1gdhy7u/experimental_flathub_release_of_newpipe_on_linux/ got a bit of traction yesterday, this is WhatsApp straight from Meta running on Linux desktop using android-translation-layer.
android-translation-layer (ATL) is a Wine-like approach to run Android applications on Linux. Rather than running an Android container like for example Waydroid does this instead implements the Android API. Note that right now it’s very much work in progress and almost no app will work yet, but the fact that they have apps like Newpipe and WhatsApp running already is very promising!
Join the Matrix chat at #android-translation-layer:matrix.org and follow along!
You’re right, you can’t run the Android (or iOS app) twice. If you want a second device running WhatsApp you’ll need the web app.
I think you can link a second Whatsapp app, similar to the web client. your primary one needs a webcam to read the QR code though