You confuse rule vs procedure
Rule - units with a missile attack can shoot at chargers (under specific circumstances), possibily causing wounds and removing stands on attacking units
Procedure -
roll command,
move first stand,
move additional stand (cf. the Movement distance, Charge and Extending Frontage rules)
all stands from contacted unit(s) that are not engaged in HtH already get missile attack IF the attacking unit was in their LOS at any time during the move
roll missle attacks, applicable save, remove stand where appropriate
IF any other unit can charge an enemy based on the same order, go back to "move first stand"
There is no "rule" that says you can only shoot at attackers when they are in contact with your stands, it is a practicality of the procedure to roll them at that time, and before moving the next unit, because in those cases where stands ARE taken casualty, this may influence the next unit moving.
Note that sometimes stands get to shoot at attackers that actualy end-up outside LOS, which could be interpreted as "the shooting takes place at any point where the shooting unit can acutaly SEE the attacker.
Skaven WLC rule says adjacent units may be confused it the target unit gets hit, but it also EXPICITLY states "Skaven units can be affected when adjacent to a WLC that misfires and hits itself".
Note that the "point blank" interpretation (shooting after the contact), would also imply that attacking units "adjacent" (which does include the attackers in contact with it as well) could be confused on a misfire. But that the Skaven rules EXPLICITLY states that that applies to Skaven units.
Just make sure you and your opponent interpret the rule the same way before the situation actualy occurs.