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The nios code won't be position independant - that is only done for shared libraries.
However it could well be there to force the physical address be different from the logical address - this will affect the elf program headers.
Typically the physical and logical addresses are different when the code will be copied after being loaded, or when the memory maps seen by the cpu and loader are different.
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I must admit to be being fairly ignorant of NiosII assembler, but the comments in the boot loader Makefile claims the code is fully relocatable. That doesn't mean the same thing as position-independant, but I assumed that's what they meant, unless SOPC Builder (or whatever) relinks the code to the EPCS boot ROM base address. The boot loader code is rather special - it doesn't even have a stack!
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