Production cabinetry is usually available in 3" increments starting at 9" wide. What happens is that the linear dimensions are filled up with as many like sizes and filler strips to to the opening. This holds for upper cabinets and base cabinets.
Along those dimensions there are spaces left for appliances. Whether there is any vertical alignment from the upper cabinets to the base would be most likely a coincidence.
For custom cabinets, there is an attempt to create a pleasing visual alignment. I prefer to make continuous lengths as one cabinet if possible. Doing that makes in shop handling and delivery and installation a bit more difficult.
There can be a level of uniqueness to cabinet work. Two of mine were like that. One was done with butcher block laminate. The client wanted the pattern to match vertically from the top of the upper cabinet, down to the underside, and match back to the backsplash. Then down the backsplash to the countertop. Then from the back of the countertop to the front edge. Then down the front edge, matched vertically to the face of the base cabinet doors to the toe kick, and matched down the toe kick.
The other one was done with Palomino Leather laminate, polished copper, and polished brass. There was a 2" polished brass and a 1" polished copper stripe together inlaid to match in the upper doors and the lower doors vertically in about 30" intervals, wherever that happened.
Sorry to get off on this tangent, but custom cabinets can show craftsmanship not available with mass produced cabinets. Back to the question about individual boxes versus long integral cabinets, there may be some savings with less ends, by using dividers that share doors.