To put it more simply also, if you'd like to play with the individual parts, the SEXP ship-effect used with "Cloak/Decloak" (this is an animated effect which requires some extra table stuff but if you're using the MVPs you already have it) is what makes a ship visually invisible, the "stealth" flag is typically used for making ships untargetable, and the "no collisions" flag makes the ship intangible (including to other ships, which may not be desired, doing this to weapons only is possible but more complicated). Axem's script does the first two (as well as a lot of other things too), but does not make a ship intangible.