This page talks about testing the alternator in position. The test involves: "and connect the black and brown/green cables together...".
On the 4TR alternator control unit these are the wires coming in to the F and to the +. Connecting these two together in the connector block means that all power generated by the alternator is fed directly to the battery. The C/D ammeter gauge on the dashboard now should show a clear charging if you let the engine make some firm revolutions. If the ammeter stays quiet, the alternator generates no power.
The 4TR control unit is bypassed, and thus does not get a chance to detect that the battery is fully loaded, and thus cannot disable the field windings in the alternator anymore (by earthing them), which is its normal task.

If you want to start the engine with external battery cables, and make the mistake of connecting them in reverse polarity, you blow the alternator immediately.