Windows Installation with EFI
In MBR disks with legacy boot enabled OS installs bootloader on first 446 bytes of active primary partition. In case of EFI files required to boot are put on EFI partition. EFI bootloader applications are EFI files which should properly be put in System's EFI partition.
As for Windows installations Windows automatically detects whether the system is using EFI or legacy and installs accordingly. Usually there is also an option in modern mainboards BIOS to enable/disable EFI boot. When it is enabled for GPT disks Windows will install EFI bootloader instead of legacy bootloader which uses mbr.