[llvm-objcopy] Use physical instead of virtual address when aligning and placing sections in binary

For sections with different virtual and physical addresses, alignment and
placement in the output binary should be based on the physical address.

Ran into this problem with a bare metal ARM project where llvm-objcopy added a
lot of zero-padding before the .data section that had differing addresses. GNU
objcopy did not add the padding, and after this fix, neither does llvm-objcopy.

Update a test case so a section has different physical and virtual addresses.

Fixes B35708

Authored By: Owen Shaw (owenpshaw)

Differential Revision: https://reviews.llvm.org/D41619

llvm-svn: 323144