As the rules are written, using the Emergency Invasion Beam Stratagem to set up a unit is not considered using the Invasion Beams ability of a Night Scythe. It doesn't say "activate the Invasion Beams ability" or anything like that; it just lets you set up a unit. Therefore, Emergency Invasion Beam does not allow you to use the Enhanced Invasion Beam Stratagem. However, I think that it wouldn't be too unreasonable to play things this way with your friends.