1.- The 100 ohms resistor in the output of the LM393 to 5v is a typical pullup, yes. Its function is to polarize the output transistor collector. In the case of your example the vaue of 100 ohms is to work the LED when the output transistor of the LM393 is in OFF. When this is in ON, the voltage in collector will be 0.8v maximum and the LED does not work, because the LEDS need 1.5v typically. Other higher pullup values will make the LED look less.
2.- In my LM393 subcircuit I add a buffer to convert the output of the Standard Primitive Opamp of Simulide in Open Collector (this means that the LM393 can only be used as comparator). See it in the buffer Properties.
3.- The file 0_INVIS.png in the data folder of my LM393 subcircuit is to make invisible its background.
4.- Yes it is needed, but the package file should typically be informative of its Pinout, NEVER for operational use. In the particular case of the multicircuits and obtaining its individualized use over the LS package (Logical Symbol) it is espetially necessary that the package file does not exist or that it has another extension. This is essential to avoid collisions between the two.