The Ghost is unaffected by the Confusion spell. While there is no strong statement that all creatures affected by a spell are "targets" of the spell, I did find this on page 205 of the PHB:
Many spells specify that a target can make a saving throw to avoid some or all of a spell's effects. The spell specifies the ability that the target use for the save and what happens on a success or failure.
This seems to imply that the targets of a spell are any creatures affected by it, although it's obviously not as clear as we could hope. Another example, on page 196:
If a spell or other effect deals damage to more than one target at the same time, roll the damage once for all of them. For example, when a wizard casts fireball or a cleric casts flame strike, the spell's damage is rolled once for all creatures caught in the blast.
As backup for this, we have the Ghost's Possession ability on page 147 of the Monster Manual:
The ghost can't be targeted by any attack, spell, or other effect, except ones that turn undead[...].
Turn Undead is an AOE ability, not a targeted one. If the Ghost was still meant to be affected by AOE spells and abilities, the caveat for Turn Undead would not be necessary.
And finally, if AOE spells did affect a Ghost in the midst of possessing someone, the Ghost would be affected by every Fireball or Lightning Bolt that hit the possessed creature. In your fourth point, you asserted that this obviously wasn't the case, which I agree with. There's no reason why Confusion would work differently than every other AOE spell.
Phantasmal Killer has been errata'd
http://media.wizards.com/2015/downloads/dnd/PH_Errata_1.1.pdf
Phantasmal Killer (p. 265). The frightened target makes a save at the end of its turns, not the start
So the complete exact text is:
You tap into the nightmares of a creature you can see within range and create an illusory manifestation of its deepest fears, visible only to that creature. The target must make a Wisdom saving throw. On a failed save, the target becomes frightened for the duration. At the start end of each of the target’s turns before the spell ends, the target must succeed on a Wisdom saving throw or take 4d10 psychic damage. On a successful save, the spell ends.
IMHO DM Ruling is required here.
That successful save refers to any save for that spell or just one of the "avoid the damage" saves?
Since the errata says "the frightened target makes a save" I'd also rule that if the target has the frightened condition removed the entire spell ends.
Please note that this strict ruling makes this 4th level spell sub-part.
Feel free to give Phantasmal Killer some DM love :D
Edit:
After more general considerations and a lenghty discussion with friends I feel the need add this:
Lets consider Vicious Mockery
You unleash a string of insults laced with subtle enchantments at a creature you can see within range. If the target can hear you (though it need not understand you), it must succeed on a Wisdom saving throw or take 1d4 psychic damage and have disadvantage on the next attack roll it makes before the end of its next turn.
If cast on a creature immune to psychic damage should I roll the save?
Yes, because a failed saving throw determines two outcomes, psychic damage and disadvantage on the next attack roll. If the target fails the save it would take no damage but still suffer the disadvantage.
So, back to Phantasmal Killer:
"On a successful save, the spell ends." seems pretty clear to me.
If the save agains fear succeeds the spell ends, if it fails the spell goes on even if the target is immune to the frightened condition. This is brutally RAW.
I very much doubt this is RAI, especially considereing the wording in the errata. In any case, forgoing the first save its a bit too much.
Best Answer
I'll deal with the simplest question first - Horrifying Visage is listed under the Ghost's Actions section, so it requires an action to use. While under the effects of Time Stop, this is impossible for them.
As for the question of multiple Ghosts using Horrifying Visage, the answer is contained in the rules quote you included:
Immunity is only to a specific Ghost's Horrifying Visage, not to any Ghost's Horrifying Visage.