In general, the most secure scenario is when you only use Tor Browser on top of Workstation.
Whonix is created by design all apps are going through Tor but other apps can collect metadata to create a unique fingerprint so anonymity can be reduced to pseudonimity. But in general, it is hard to gain full anonymity. If you don’t have an alternative, then you can use any app you want with Whonix. But Tor Browser is still preferred for most kind of activities
Using XMPP + GPG on top of Tor is the most secure type of chatting I think. But if you’d like to use not only private messages but group chats then you can use OMEMO encryption. Note that group chats are stored on XMPP servers.