Hm... I see that MC6847's color artifacting is enabled via a UI config option, which is available to the code as a port:
Code
INPUT_PORTS_START( m6847_artifacting )
    PORT_START("artifacting")
    PORT_CONFNAME( 0x03, 0x01, "Artifacting" ) PORT_CHANGED(artifacting_changed, NULL)
    PORT_CONFSETTING(    0x00, DEF_STR( Off ) )
    PORT_CONFSETTING(    0x01, DEF_STR( Standard ) )
    PORT_CONFSETTING(    0x02, DEF_STR( Reverse ) )
INPUT_PORTS_END
Then...
Code
    /* are we artifacting? */
    artifacting = input_port_read_safe(machine, "artifacting", 0x00) & 0x03;
    if (artifacting == 0x00)
        return;
...else (artifacting != 0x00), proceed to produce the artifacting effect.

I could do something similar, add a UI config option so that joystick is only mixed to the keyboard if the user chooses that.

(Unless, of course, there is already something like that already implemented in MESS' core.)

Whaddya think?