Resize partition by 1 or 3 MiB is not possible

Partitions need to be aligned and when misaligned will error out so tools will align it automatically. parted the backend of gparted has an automatic alignment but also an option to turn it off.

parted /dev/sda
align-check opt n

where n is the partition. Also from the manual there are options for this:

-a alignment-type, --align alignment-type

Set alignment for newly created partitions, valid alignment types are:

• none Use the minimum alignment allowed by the disk type.
• cylinder Align partitions to cylinders.
• minimal Use minimum alignment as given by the disk topology information. This and the opt value will use layout information provided by the disk to align the logical partition table addresses to actual physical blocks on the disks. The min value is the minimum alignment needed to align the partition properly to physical blocks, which avoids performance degradation.
• optimal Use optimum alignment as given by the disk topology information. This align to a multiple of the physical block size in a way that guarantees optimal performance.

Most tools use a default 1Mb alignment. But...

• on MBR disks: the size or offset parameters are rounded up to cylinder alignment.
• On GPT disks: the size or offset parameters are rounded up to sector alignment.