Extended partition does not start on physical sector boundary on 512e (emulated 4k) hard-drive

Question

My fdisk -l output tells me that my extended partition (sda4) is misaligned. But partitions inside it are aligned (their start sector is divisible by 8). Will the misaligned extended partition somehow impact the performance?

Disk /dev/sda: 1000.2 GB, 1000204886016 bytes
255 heads, 63 sectors/track, 121601 cylinders, total 1953525168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disk identifier: 0xb82c3054

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048      206847      102400    7  HPFS/NTFS/exFAT
/dev/sda2          206848   419635199   209714176    7  HPFS/NTFS/exFAT
/dev/sda3       419637248  1806721023   693541888    7  HPFS/NTFS/exFAT
/dev/sda4      1806723070  1953523711    73400321    5  Extended
Partition 4 does not start on physical sector boundary.
/dev/sda5      1806723072  1814720511     3998720   82  Linux swap / Solaris
/dev/sda6      1814722560  1854719999    19998720   83  Linux
/dev/sda7      1854722048  1953523711    49400832   83  Linux

Answer 1

No; that warning is a bug. It's actually impossible to properly-align an extended partition on a modern disk, because the data structure it contains is only one sector in size. Thus, no matter where it's placed, writing that data structure will write just one sector, resulting in the sort of inefficient write operation that's the reason for aligning partitions in certain ways. Fortunately, this doesn't really matter, since writes to the extended partition (as distinct from the logical partitions it contains) are extremely rare. Furthermore, we're talking about just one sector, so even when you do write it, the speed reduction is not likely to be noticeable.