The major difference is that Microsoft don't own the internet, WhatsApp do own their own XMPP service.
Taking that even further, they pay to keep their XMPP servers running, WhatsApp Plus don't. Allowing third party access to such servers not only puts users at risk, but can also have an impact on normal WhatsApp users because of how WhatsApp Plus works and accesses their servers.
Slashdot Mirror
The major difference is that Microsoft don't own the internet, WhatsApp do own their own XMPP service. Taking that even further, they pay to keep their XMPP servers running, WhatsApp Plus don't. Allowing third party access to such servers not only puts users at risk, but can also have an impact on normal WhatsApp users because of how WhatsApp Plus works and accesses their servers.