It does not matter which id the fat efi partition has, certainly you could use ef with mbr or add the bootflag with gparted but it really does not matter as soon as you use efibootmgr. Also the normal alignment is now 1M, which is default for gparted now, no need to do that manually... Btw. the interesting thing is that you can use efi direct boot even with intel raid (via mdadm not dmraid as that has got no gpt support), i did a win uefi install first and then linux, i could boot like that:
Note that win8 will use the 2nd partition for efi boot code.
efibootmgr -c -d /dev/md126 -p 1 -l '\EFI\KANOTIX\linux.efi' -L 'Kanotix 64 Pure' -u 'initrd=EFI\KANOTIX\initrd.img root=/dev/md126p4 quiet'