Your disks are either 512e (512 sectors on SAS/SATA interface) or 4k native (4k sectors on SAS/SATA interface), and unfortunately there is no way to change that via software or jumpers etc. You select the transfer mode when you buy the disks. Buy 4k native disk if you have adapter that supports 4k native on interface.
Update: and, once again, the disks never "fallback from 4kn to 512e" etc. The disks are either 512e - it means they will always send data in 512 sized sectors over SAS/SATA interface, or 4kn, it means disks will always send data in 4k sized data over SAS/SATA interface, and it depends only on disk, not on RAID adapter capabilities. The difference between 512n and 512e is that on the physical media sectors are sized as 512 for 512n, and 4k for 512e (disk chip translates each 4k sector on plates into 8 x 512 sectors on interface), on the interface 512e disk will always transmit only sectors at 512 bytes, no matter what adapter it is connected. The part number differ for 512e and 4kn disks, for example:
ST6000NM0014 - 6TB SAS drive with 4k sectors on SAS interface (called 4kn drive);
ST6000NM0034 - 6TB SAS drive with 512 byte sectors on SAS interface (called 512e drive)
both of these have 4k sectors on disk media, so care must be taken about sector write alignment in 512e case.
And you can still buy 512n disks, for example:
ST4000NM0023 - 4TB SAS drive with 512 byte sectors on interface and 512 sectors on media, so no need to care about sector alignment for this drive.
The RAID adapters fall intro 3 categories:
a) the oldest ones that do not know about 4k sectors - they work with 512n and 512e disks, however issues may arise with write performance if writes are not aligned by 8xsector boundaries on 512e drives,
b) the not so old ones that know about 4k internal sectors and about 512e emulation, but only work with 512 sectors on interface - less problems with alignment as controller cares about that,
c) the very new ones that are able to work with 4k sectors on interface. Only these will work with new 4kn disks that pass native 4kb sector as 4kb sector onto SAS/SATA interface.
Also, only Windows 8, 8.1 or later OS support 4kn drives (for server, 2012 or later version). Majority of old utilities that directly work with disks will NOT work properly with 4k sectors as they assume sectors are always 512 byte sized. instead of checking.
So, to avoid any confusion with alignment and get the maximum performance, use new 4kn drives, new 4kn enabled adapters, and new OS.
I think this statement below is not correct:
"certain 4kb-native disks may choose to support 512-byte emulation. If they support 512-byte emulation, they can switch between this mode and 4kn depending on what the disk controller supports; they'll prefer 4kn, but fall back to 512e if they have to".
Sector size is fixed in the factory. I am not aware about any drive that is able to automatically change sector size on interface depending on RAID adapter capabilities. What I see in Seagate order systems are very separate part numbers depending on sector size on interface. Impossible to change sector size after disk is ordered (could be possible by some hacking, changing disk firmware, etc. but not officially supported). So if your drive is 512e it will always send only 512 byte sectors on interface, and never 4k sectors. If your drive is 4kn, it will always send only 4k sectors on interface and never 512 sectors. You decide only when ordering, as its different part numbers.
The possible drive formats are (the number indicates sector size on interface):
512n - 512 on disk, 512 on interface (simple)
512e - 4k on disk, 512 on interface (performance complications possible on old systems)
4kn - 4k on disk, 4k on interface (simple, best interface performance, do not work on old systems)
n or e means if specified sector size on interface is native disk sector size (n), or emulated size (e).
And the answer is: your disks are 512e disks (as they work with adapter that does not support 4kn disks), they are not 4kn disks. Your 512e disks will never use 4k sectors on interface with any RAID adapter. BTW, only the very new 6TB drives from Seagate are possible in 4kn format, and new 6TB and 8TB from HGST also can be ordered as either 512e or 4kn. All drives up to 4TB before were only available in 512e or 512n, I was not able to purchase any 4kn drive for testing before this September.
My personal recommendation is to use LSI adapters. Most compatible with best error reporting from anything I tested, and best performance. With latest firmware release, fully support 4kn disks. I am using many Smart Array adapters from HP also, as they come with HP ProLiant servers, but still no information if and when SmartArray adapters will support 4kn disks. Only host bus adapters mentioned in release notes - very recent firmware update enables support for 4kn disks. So, still 4kn disks are very new.
Hope I helped to make it clear.