Is there any rhyme or reason the 24-120 should be made the other way round, with the focus ring nearest the body?
If the focus and zoom rings are directly connected to the focus and zoom mechanisms inside the lens, as is the case for many lenses, then the relative placement of those mechanisms determines how the rings need to be placed in order to retain a full range of motion. And how those mechanisms are placed inside the lens is determined by the design choices that the manufacturer made in creating a lens which meets a set of goals.
That is, if the optical design places the lens group(s) involved in focussing in the rear of the lens and the zoom group(s) in the front, you cannot directly connect the rings that control them while placing the rings in the opposite order because they would interfere with each other or limit each other's range of motion to around 180°. Focus-by-wire allows the focus ring to be physically decoupled from the focus mechanism and therefore let it be placed either in front of or behind the zoom ring regardless of how the focus and zoom mechanisms are placed. Focus-by-wire has it's own tradeoffs, though: it's only possible if the lens (or body) has an autofocus motor; it's less reliable; it may add cost; it may be less appealing to customers.
Maintaining a consistent placement of the focus and zoom rings might be one of the considerations that goes into the design of a lens, but it's probably not high on the list of priorities. Much, much more important are considerations such as optical properties, ease of manufacture, reliability, and cost.
Looking through Nikon's lens line-up, it does seem to be fairly arbitrary.
Placement of the rings might appear arbitrary, but it's surely not capricious. Consistency in the order of the rings clearly just isn't as important as other design considerations.
Is it something you just get used to over time?
Sure, the more you use the lens, the more you'll get used to it. Consider slowing down a little bit and trying to be more purposeful in your actions. Some aspects of photography, like sports or fashion, benefit from lots of practice with specific gear in order shoot quickly. Macro and still life photography don't really fall into that category, though, so just give yourself an extra moment to look at what you're doing. That'll allow you to develop the right habits without frustration. Also, think about using touch rather than position as your guide -- most zoom lenses have a big, beefy zoom ring and a not-so-big focus ring, and the rubber texture on each is generally different.
I shoot always in manual mode
Assuming you mean manual focus, that's another thing you might want to reconsider. For macrophotography, a lot of the time you hardly use the focus ring at all, and instead focus by adjusting the camera's position using a focussing rail. And there's little reason beyond machismo to insist on only using manual focus; if speed is important to you, you should be practicing with autofocus as well because the camera can focus much faster and often more accurately than you can.
