Oh for the love of god....
As for the Portal of Exile: it can hit flyers... nothing stops it from doing so because it does not target then, and so does not have to snap fire (in fact the only way that it can ever be made to snap fire is if you fire the particle whip). It can, however, only damage FMCs since it does not affect vehicles anyway (models without a strength value are immune).
As for Zion's: "It's not a matter of if the marker TARGETS the Zooming Flyer but how hits are RESOLVED against it."
This is just plain wrong... it is exactly a matter of targeting the flier. The snap fire rules come into play when you are firing a shot (1- terror from the deep isn't a shot) at a flier (2- terror from the deep does not target anything)...
Now if you were going to make a BS argument you could try claiming that since its a pseudo-shooting attack Terror from the Deep must be a weapon and therefore fliers are immune (since it would be a large blast weapon)... it would sound slightly less stupid.
I know you're fuming on your end of the keyboard, and I didn't bring fluff anywhere near this one, I'm just trying to get a better handle at understanding these new rules. Hence opening a dialogue with other people. I will admit I got irked about the "template" verus "marker" bit coming up more than once, but I'd stated that that wasn't what was effecting my reasoning on this as it could have been called anything and in this situation I'd still said "no".
Alright, I'm going to trying and be more clear and direct this time while addressing your points:
1. Shooting Attacks That Don't Target Zooming Flyers Still Hit Them.
I both agree and disagree with this statement. If the model firing it (or the weapon in question being fired) has the "Skyfire" rule, then yes, this statement is true as far as I understand the rules right now, but there is a caveat to this. And again, I refer to the "Hard To Hit" part of page 91 (this time with my own emphasis): "Shots resolved
at a Zooming Flyer can only
as Snap Shots (unless
has the Skyfire special rule, as described on page 42)."
Now please note that this says "resolves" not "targets", and as I previously stated this was a big part of why I came to the conclusion I did. It doesn't matter how the shot targets a Zooming Flyer as per the rule but how the shot is resolved against a Zooming Flyer as per the rule. And since the Mawloc doesn't have Skyfire I don't think it's Terror From the Deep ability can affect Zooming Flyers.
2. Snap Fire Only Applies When Targetting the Flyer
I disagree, targetting is done when you place the marker with the intent to hit the Flyer, the actual Snap Fire comes into play when resolving the hit. And since you can not auto-hit a Zooming Flyer with a Shooting Attack (since it resolves all Shooting Attacks from models and/or weapons that do not have the Skyfire rule as Snap Firing Shots the hit is negated by the actual Snap Fire rules).
3. Terror From the Deep Being a Psuedo-Shooting Attack
I actually believe it is, as there are two ways to hit models: by shooting, or in assault (this includes auto-hitting models through other means). Since the Mawloc doesn't enter combat with any unit it attempts to eat, and the attack allows cover saves (which are only given to shooting attacks) I believe that Terror From the Deep is a Shooting Attack. It (like Vector Strike) is not a weapon, but an ability that is treated like a Shooting Attack for the purposes of the rules and thus is the other big reason I say that the attack can not affect the flyer.
4. Zion's Idea is Stupid
I also disagree as I clearly stated my line of logic, the rules I was referencing to show where I was drawing my conclusions from when I was puzzling over the rules to see if I could figure this one out. I'm willing to discuss this in a civilized manner as I do believe I'm supported by the RAW, but I'm willing to discuss it, not argue it. And I still don't care if it's a marker or a template because it's a) a marker and b) doesn't affect my train of thought that I used to reach my answer.