This feature is intended as a convenience when JMP uses inappropriate axis settings by default. It enables your to modify the axis settings, including reference lines, and save the custom axis as a column property. The column property should be respected in any plot using that data column. It over-rides the axis in such a plot.
So this behavior is not a bug. The plot axis and Axis column property are working as intended. The typical use case did not consider that someone would want to ignore or update the axis settings or the Axis column property. You might want to click JMP Wish List in the menu above to see if what you want has been suggested. If so, kudo it! If not, then add a request.