Here is the lowdown, fdisk does not assume you have advanced format probably if your disk has a logical of 512 and a physical of 4K.
So it will likely print
Partition x does not start on physical sector boundary
fdisk is wrong, your partition may or may not be aligned
In reality, just by running fdisk with the new alignment should tell you if it is really miss aligned, or fdisk is miscalculating
fdisk -b 4096 -u /dev/sda
Now try and print, if you still see that message, then it is miss aligned, otherwise you are fine