SocksPorts and ControlPorts should be stored in a set, not a list
When using domain sockets, Tor Launcher needs to launch tor with a specific unix-domain SocksPort. The SocksPort is initially not in the torrc file (as the full path is not known before installation), so Tor Launcher passes the SocksPort setting in to the tor process via the tor command line.
Tor Launcher also calls saveconfig later in the session, such that the SocksPort will be saved to the torrc. So the next time Tor Launcher launches, passing the SocksPort to the command line is a duplicate of the previous SocksPort, now loaded in from the torrc. Tor then shows an error.
For an example, see ticket:20761#comment:11. More background is in #20761 (moved) as well.
I think a solution to this would be for tor to store SocksPorts (and similarly, ControlPorts) in a set rather than a list. So if the command line or a torrc or a setconf invocation specifies a redundant SocksPort setting, no error is thrown but the redundant setting is gracefully ignored. And only a single copy of a given SocksPort setting should be saved to the torrc when saveconfig is invoked.