This is a difficulty that comes up in a lot of RPGs actually, including way back in the early editions of D&D (from which Rogue Trader gets its Disengage-to-avoid-bonus-attack rule).
Think of the round as being full of position and weapon maneuvers and potential attacks, but the roll is only made for the pivotal attack opportunity for which all the the feints and parries and ducks and weaves were softening up the enemy. In this way, the roll is an abstraction of all your careful efforts during the round. See the "Combat Abstractions" sidebar on page 234, where the rules instruct the reader to think of a combat round this way:
[Combatants] are constantly side-stepping, twisting, and ducking, to avoid attacks or assume more favourable combat positions.
And then, when your opponent suddenly flees without carefully disengaging, you can just straight up stab at them because they just gave you a golden opportunity for no effort on your part.
As for the strolling NPC, that's legal in Rogue Trader, apparently as a design choice. The only way you get your "opportunity attack" against a moving target that hasn't used Disengage is if they were already engaged in melee with you, and becoming engaged due to moving only happens when the movement ends adjacent to an opponent (Move p. 241; Engaged in Melee p. 247). Since they're not stopping, they're not engaged, and you don't get the free attack. (Contrast this with another system that uses the "Disengage" design for "opportunity attacks": in early D&D, you become engaged immediately upon becoming adjacent, making opponents "sticky" and enabling them to control their adjacent squares by forcing a Disengage to move again.)
Why that's legal is an aesthetic design choice, as far as I can see. You can rationalise it with a story, or you can object to it on tactical design grounds — but regardless it's RAW. The easiest rationalisation is that opponents who aren't anticipating the need to physically stop someone are unable to do so — they're busy with whatever else they decided to do that round and the opponent ducks and weaves through the battlefield to wherever they're going.
The tactical objection is that this makes it hard to control the battlefield! That's reasonable, but the intuition is likely conditioned by Pathfinder's (unrealistic but functional) way of managing battlefield control.
To accomplish movement control in Rogue Trader, instead of it happening passively as in Pathfinder, you have to use a mix of passive and active tactics. Passively, you can either completely block passage by standing shoulder-to-shoulder, providing no space for an opponent to move through; or you can spread your forces out such that their movement has to end adjacent to one of you. Of course, that passive kind requires a lot of bodies and coordination. Active prevention can be done more solo but with more effort investment, by anticipating the need to stop an advance — which is what the story above implies is the solution — and using the Delay action to attack the incoming opponent. Because attacking someone immediately makes them engaged in melee, they won't be able to continue their movement after your delayed attack, and will furthermore be forced to use Disengage later to continue toward their position objective.
It looks like, yes, it does apply when starting on the ground next to an enemy. There's no restriction on it about starting the turn in flight, nor any rule elsewhere that would make starting to fly not count as flying for the first square of movement.
However, a DM who cares about what abilities actually do fictionally and what they actually look like is within their rights to rule that it can only be used while reasonably doing an actual flyby. Since it's a DM-controlled monster, that would be ruling in the PCs' favour too, so it's unlikely to be a point of contention.
A DM heading a group who wanted to play in more of a D&D 4e style, with abilities doing only and exactly what they say — a playstyle that 5e can support with some thought — would also be perfectly in their rights to say that Flyby can be used during takeoff and landing. Since this is unfavourable to the PCs though, a DM who isn't playing in a group that explicitly wants that kind of combat style might want to reconsider playing this ability literally.
Best Answer
Yes
I'm not sure why there is any doubt about this:
If the putative rogue has a reach of 5 feet or more, a reaction available and the target is visible then if the target leave's the rogue's reach using their own movement then they rogue can launch an Attack of Opportunity.