Can a Windows 2016 server provide two PXE boot sources?

[NiKiZe]

First of, no EFI implementation should support booting from NTFS it is FAT32 only.
The solution here is to have a 512MB-1GB FAT32 partition on usb device that contains all the boot files, and then have another partition that is NTFS that contains the full sources directory.
It seems you got this working in the rufus issue, but be sure it is actually using EFI, and has not fallbacked to pcbios mode (which is the only way that it should be able to boot from a NTFS filesystem)

If you want to have boot windows PXE services and iPXE for efi then no, you will have to choose one or the other.
With iPXE you can always chain into the other, but not really trivial.
But before that, build the ipxe.efi, or snp.efi which you can copy to a USB drive as bootx64.efi and then use that to test things out before modifying the dhcp server to send these out. (see http://ipxe.org/appnote/buildtargets for how this is done, and there is also some prebuilt ones at boot.ipxe.org)