Since a recent update you can enable private message routing which means you never connect to any servers but your own. Your incoming SimpleX server will then forward your outgoing message to the incoming message server designated by your communications partner. 

On the other hand if you can enable a Tor proxy in SimpleX I don't really see any harm in connecting to the other persons SimpleX server directly. The server will only see your Tor IP address (often times not even that when your connect via its hidden service, which most offer).

I would even argue that connecting directly over  Tor is more private in the situation where you host a small personal SimpleX server. As a evil SimpleX server:  If I see your SimpleX servers' IP connecting I can expect it's you delivering a message. If I see a random Tor exit IP, the anonymity set is much larger.