Sav
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Flying over and entering is the same thing (in terms of pathfinding), but in SoD, this is only different for towns.
Almost all objects are like this. Specifically, these are all objects where you cannot enter the trigger cell from above, and conversely, you cannot go up from it (even if there are no impassable cells above). The main exceptions are pick-up objects and garrisons (which are not present in HotA anyway).
This issue only occurs with trigger cells of objects; regular impassable cells can be flown over without any problems.