It is what it is.
There may have been a very good reason why Apple changed the relative location of the internal smart cover magnets.
The internal arrangement of the new iPad Mini maybe different inside now, from previous Mini models, with additional hardware needed for the Apple Pencil and the extra screen layer needed, as well as, and any other additional components on the motherboard that are needed to accomodate Apple Pencil functionalities, such that the location of the internal cover magnets needed to have their location changed slightly.
We do not know anything for sure, but I am betting that this is the reason for Apple having to change the relative location of the internal smart cover magnets.