How does a multimeter sense whether it is measuring single or 3 phase voltages?
There is no "intelligence" in a multimeter and, for AC measurements the voltage it is measuring is converted to an equivalent DC voltage suitable for a standard moving coil meter mechanism. On digital multimeters the voltage is also converted to DC and fed to an analogue to digital converter - basically the digital electronics has no idea whether AC or DC is being measured.

It is up to the user to decide, based on experience if the voltage is likely high enough to be line-line or line-phase voltage.