When you format the drive and selected 4096 bytes, it specifies the allocation unit size, which is completely different from the physical sector size.
Of course formatting the drive does not alter the physical sector size in any ways, just specifies the OS about how much physical sector(s) should be used in each allocation units.
If you select the partition (bottom left area) in Hard Disk Sentinel, then on the rightmost informational area you can verify the selected "Allocation Unit Size" (which is connected to the actual partition, not the physical drive itself).
3 TB+ drives should have 4096 bytes sectors of course.
If 512 bytes reported, it means that the current driver / adapter / enclosure may use an older, compatible mode to address the complete hard disk. This may cause incompatibility issue or performance degradations.
If you can use Report -> Send test report to developer option in Hard Disk Sentinel, it may help to check the current disk controller, driver, connection - to verify the situation.