Well, there are two types of so called "Emulation". Since legacy systems support only 512 logical sector size, the ATA standard implemented aditional information of physical sector. So the 4kB sector drive reports 512B logical sectors and communicate with OS using 512B sectors, but also reports 4kB physical sector size, so modern operating systems are able to align partitions with 4kB boundary.
What idiots in WD did? They crippled this standard mechanism by reporting 512B logical and 512B physical, or not reporing Physical sector size at all. This means any operating system, including 4kB-aware one, is not able to recognize, what physical sector size HDD realy use.
The jumper you mentioned does not on and off the 512B emulation, but it moves LBA numbers +1. Obsolete Windows XP start first partition at LBA63, which is not aligned, when you use 4kB physical sector. Such a physical sector contains 8 logical (512B) sectors, thus you have to start at multiple of 8. Starting from LBA0, it is LBA8, LBA16, LBA24 etc... So with WD jumper LBA0 is marked as LBA1 etc.... So the WXP starting point LBA63 is physicaly LBA64, and the partition is alligned. This is really ugly hack, since you can not properly install other moder systems on such jumper-crippled drive.
The problems described are mainly Windows driver related (binary chipset drivers from Intel, AMD, nVidia etc...). Updated drivers are able to operate larger drives.
This is not true. GPT drives can be booted on BIOS system (non-EFI boards). BIOS does not forbid this! This is problem of obsolete Microsoft (in fact MS-DOS) booloader and partitioning scheme.