Tor runs on StartOS by default. On StartOS v0.3.5.1 the server runs tor in the background and all services are enabled only for remote access via tor.
Some services reach out over clearnet because this is faster, easier or better in some way. Such services typically have an option to force them not to do this and instead reach out via tor and eventually an exit node back onto clearnet.
An example of this is Bitcoin. While peers can only connect to you over Tor, your instance of Bitcoin reaches out to clearnet peers on the network to download blocks… because this is faster.
Everything you’ve done is fine.