The warn is bit distressing that HDD's ESP does not start on physical sector boundary as its logical contradicts its physical sector
Code:
$ sudo fdisk /dev/sda
Welcome to fdisk (util-linux 2.35.2).
Changes will remain in memory only, until you decide to write them. Be careful before using the write command
Command (m for help): p
Disk /dev/sda: 931,53 GiB, 1000204886016 bytes, 1953525168 sectors
Disk model: TOSHIBA MQ01ABD1
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: gpt
Disk identifier: 25C80B90-7985-4FBD-A165-6978F5C06A97
Device Start End Sectors Size Type
/dev/sda1 2048 923647 921600 450M Windows recovery environment
/dev/sda2 923648 1128447 204800 100M EFI System
/dev/sda3 1128448 1161215 32768 16M Microsoft reserved
/dev/sda4 1161216 51568639 50407424 24G Microsoft basic data
/dev/sda5 51568656 1749237523 1697668868 809,5G Microsoft basic data
/dev/sda6 1749237524 1750159359 921836 450,1M Microsoft basic data
/dev/sda7 1861302272 1870741503 9439232 4,5G Linux swap
/dev/sda8 1786853376 1839284223 52430848 25G Linux filesystem
/dev/sda9 1750159360 1786853375 36694016 17,5G Linux filesystem
/dev/sda11 1839284224 1861302271 22018048 10,5G Linux filesystem
/dev/sda12 1870741504 1953525134 82783631 39,5G Microsoft basic data
Partition 6 does not start on physical sector boundary
...
ie.
/dev/sda6 1749237524 1750159359 921836 450,1M Microsoft basic data
How should it be solved by doing in that particular partition as many work as possible and in the way having as little impact to the others as possible when fixing it, yet still the priority is it must be getting fixed even if it must involve great work or modifications ?