War Caster lets you cast a spell instead of an opportunity attack, which is made just before the creature leaves your reach. If your reach is 5 feet and you use War Caster to cast a ranged spell attack then, yes, the attack is made with disadvantage.
If you have a natural reach greater than 5 feet, then the attack is made when the creature is more than 5 feet away, so this doesn't apply. Similarly, it doesn't apply to melee spell attacks or spells that use saving throws. You are also good if you have the Crossbow Expert feat.
RAW No, flanking's only conditions are explicitly related to physical position
When a creature and at least one of its allies are adjacent to an enemy and on
opposite sides or corners of the enemy's space, they flank that enemy...
So, RAW say it has to be adjacent. No other conditions are listed besides position.
Defining Adjacent
Adjacent is not defined anywhere in the game as a game term, but it is used a lot. All the instances I have found of the term adjacent definitely imply only one meaning: that two things are immediately next to each other. For example:
On describing the rules for counting ranges on a grid the PHB says:
Ranges. To determine the range on a grid between two things—whether creatures or objects—start counting squares from a square adjacent to one of them and stop counting in the space of the other one. Count by the shortest route.
The word adjacent here clearly only makes sense when read as "the square physically right next to".
I cannot find a single example in any of the rule books where the word adjacent was used to indicate anything other than immediate physical proximity to another thing so it would be incredibly dubious to try to read it that way here.
Similar discussion from designer and possible intent
Jeremy Crawford also touched on this subject:
Q: Polearm Master fluff say you can keep your enemies at bay with reach weapons is not really true if attack is when adjacent
A: On the grid, the target is adjacent if you're using a quarterstaff,
but 5 feet away with the [Polearm Master reach] weapons.
In this example, Jeremy reinforces the idea that "adjacent" is "immediately next to". Not only that, but note that he says that someone 5ft away from a reach weapon is 5 feet away. The strong implication being that they are not considered adjacent.
Conclusion
Bringing this back to flanking specifically, the rules do not even hint at reach being a factor. It doesn't even say you have to be able to make attacks. Just allies adjacent to an enemy on opposite sides or corners.
Best Answer
Yes, Melee Spell Attacks benefit from the Optional Flanking Rules.
Why? That's because flanking grants advantage on Melee Attacks....and a Melee Spell Attack is a Melee Attack. Just as Ranged Spell Attacks are Ranged Attacks.
IF the rules singled out Melee Weapon Attacks, then this would not work.