There are no unsolicited inbound connections except hidden services when you set some up. (Different Tor Hidden Services are automatically stream isolated.) Solicited (related) incoming connections are stream isolated by Tor. As I understand, answers for requests come in the same way through the Tor network they were sent. They don't take some random way back. That is up to Tor. None of this is specific to Whonix.
Whonix-Gateway also uses transparent proxying for Whonix-Workstation. All applications on the workstation not configured to use a SocksPort by socks proxy settings or forced to use a SocksPort by a socksifier (such as uwt/torsocks) will be routed through Tor's TransPort. These are stream isolated form all connections using Tor SocksPorts. But inside the TransPort these are mixed up and cannot be further stream isolated. The transparent proxying feature can be optionally disabled, see Whonix documentation on how to do so if you want to do that.
( https://www.whonix.org/wiki/Stream_Isolation )
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I am a maintainer of Whonix.