It appears the normal placement of NPCs and Shapes can affect how walls and some items overlap. It seems to change the precedence, if there is such a thing, so that items and wall corners appear to shift.
In the attached screenshot, when the automation in Flindo's shop (NPC12) is away from the west side the fishing rod is under the table's corner. When he is vertically aligned with them, the fishing rod appears entirely above the table. A diagonal line of pixels in the corner also appears different. This does not happen in the DOS game.
You can also see this weird wall behavior in the MageLord's kitchen by moving the west table or the milk canister away from the window. Oddly enough, the wall overlapping that table in the lower west side of it appears in the DOS game, even if it looks wrong. The corner change does not, however. If you move the wall piece that overlaps that table in Exult and put it in the same starting spot, it will place down correctly so the table corner is not clipped without moving anything else.
Finally, if you place the bottle or milk canister on the barrels and move the barrels, the bottles stay at Z-2 instead of gracefully "falling" down to Z-0 as they do in the DOS game.
Steps to recreate:
Start a new game.
Teleport to NPC 12's location.
Here's another example of the items further north overlapping items to the south that they shouldn't appear over the top of; the chairs.