[llvm-objcopy] -O binary: align sh_offset for section changed from SHT_NOBITS

For a SHT_NOBITS section like .bss, its sh_offset is typically not
aligned by sh_addralign. If it is converted to SHT_PROGBITS by
`--set-section-flags .bss=alloc,contents`, we should conceptually align
it when computing the output size for -O binary. Otherwise the output
size may be smaller than GNU objcopy produced output.

* binary-no-paddr.test has a case with non-sensical p_paddr=1 which has
  a changed behavior. Update it.

Close https://github.com/llvm/llvm-project/issues/55246

Reviewed By: jhenderson

Differential Revision: https://reviews.llvm.org/D128961