For your other question, .ELF is converted to .flash (Motorola S-Record).
The .POF (Programming Object File) is special from Altera to their FPGA. You might not find information about the structure.
But
altera give tools to create a .pof with the .sof(to configure fpga), and flash (with special boot loader). That is in the tutorial you are reading.
You download the .POF to an EPCS serial memory. So it will be size-limited (the size is not a constant because of an eventual "compression").
Nios can execute the .ELF as is. This is what you do when you "Ran as hardware" from Eclipse NIOS II SBT. It executes from RAM directly.
When the program is in FLASH, the boot loader tells NIOS to first copy the content to RAM and then Nios executes from the RAM.