AFAIK, whatsapp is still dependent on your mobile being the primary source. It has "link a device" feature, which has some of the features but cannot be used as an independent client. For example if you're using the web version and want to see some old chats, you can't unless you use it from your mobile. WhatsApp's encryption keys are tied to the device, not the account. In Matrix, encryption keys are tied to the user's account, not the device, and thus it wont be an issue.