Necropolis or Castle (Which one is stronger?)

Mobility is one of the most important factors in HoMM3, which is why the Logistics skill is so highly valued.

Absolutely. Mobility is a cornerstone of success.

However, the movement range, which you hint at when discussing the advantages of Castle, is not the only determining factor in mobility. Movement management is a combination of many factors. And you undoubtedly know this.

For example, skillful use of chains of hired heroes (for transferring troops and artifacts), timely and reasonable use of dismissal (dismissing/fleeing followed by hiring in an external tavern on the other side of the world), manipulating the arrangement of troop stacks in a hero's army (sometimes, only one correct troop arrangement allows you to avoid movement penalties on the terrain even without the Pathfinding skill), and so on.

All of this can negate the advantages of your opponent's logisticians, who only have it over direct distances. And slow Necropolis units may not be inferior in terms of territory capture speed, even without Logistics. Sometimes, opening a path to an external tavern at the cost of "meat" is much more important than moving fast troops across already cleared territory. And Necropolis units can handle this more effectively.