Soft Cover
Soft cover is cover, except with the differences that it says. Emphasis mine:
Creatures, even your enemies, can provide you with cover against
ranged attacks, giving you a +4 bonus to AC. However, such soft cover
provides no bonus on Reflex saves, nor does soft cover allow you to
make a Hide check.
That's pretty clear. It says flat out that it provides cover against ranged attacks, with the exceptions listed. AoO's are not listed as an exception, so the Cover rules apply.
AoO's Are Blocked
From the cover rules:
To determine whether your target has cover from your ranged attack,
choose a corner of your square. If any line from this corner to any
corner of the target’s square passes through a square or border that
blocks line of effect or provides cover, or through a square occupied
by a creature, the target has cover (+4 to AC).
Here's your example:
C <-> F1 <-> F2
Assuming those are all medium creatures, there is no line between C and F2 that doesn't go through F1's square, so cover applies.
When making a melee attack against an adjacent target, your target has
cover if any line from your square to the target’s square goes through
a wall (including a low wall). When making a melee attack against a
target that isn’t adjacent to you (such as with a reach weapon), use
the rules for determining cover from ranged attacks.
This says we use the ranged rules for a reach attack, so it has cover.
You can’t execute an attack of opportunity against an opponent with
cover relative to you.
Since it has cover, we can't do an AoO.
But! Large Creatures
Now consider this scenario:
--------- 1234 = large creature
-12FG---- F & G = medium creatures
-34------
---------
Same thing as before, they're adjacent. Except C is now large. The rules say that a large creature gets to pick one of its squares to determine cover.
To determine whether your target has cover from your ranged attack,
choose a corner of your square.
It can use #4 (as it can use any of its squares), and from that square it has the ability to hit G without going through F's square. As a result, G no longer has cover and the large creature can make an AoO.
That's also mentioned in the cover rules:
Any creature with a space larger than 5 feet (1 square) determines
cover against melee attacks slightly differently than smaller
creatures do. Such a creature can choose any square that it occupies
to determine if an opponent has cover against its melee attacks.
Similarly, when making a melee attack against such a creature, you can
pick any of the squares it occupies to determine if it has cover
against you.
On the upside, if G has reach, it can choose #4 as it's square as well, and it can attack the large creature without F being cover.
Best Answer
Because they are different.
Note, the water described in a marsh terrain is a "deep bog". The water described in aquatic terrain is just water. The environments are intended to be different and thus have different rules. The rules are not "complimentary" or additive.
Total cover for being underwater is somewhat of an oversimplification of refraction and the resistance provided by the water. I have hunted carp from the bank with a bow and, at least for me, it is largely blind luck determining where to aim. To be fair, on a sunny day, with clear water, with a fish very close to the surface, you can actually target them by shooting "beneath" them, if that makes any sense, but it is extremely difficult to know how much to correct for the refraction. Hence in the rules, it becomes "total cover". Add some turbidity and any significant distance from the surface or poor lighting and it effectively is total cover.