https://sourceware.org/bugzilla/show_bug.cgi?id=28689
--- Comment #2 from H.J. Lu <hjl.tools at gmail dot com> ---
One problem:

Elf file type is EXEC (Executable file)
Entry point 0x600000
There are 7 program headers, starting at offset 64

Program Headers:
  Type           Offset   VirtAddr           PhysAddr           FileSiz  MemSiz
  Flg Align
  LOAD           0x000000 0x0000000000400000 0x0000000000400000 0x0001f8
0x0001f8 R   0x1000
  LOAD           0x200000 0x0000000000600000 0x0000000000600000 0x000001
0x000001 R E 0x1000
  LOAD           0x400000 0x0000000000800000 0x0000000000800000 0x002000
0x002000 RW  0x1000
  NOTE           0x0001c8 0x00000000004001c8 0x00000000004001c8 0x000030
0x000030 R   0x8
  TLS            0x400000 0x0000000000800000 0x0000000000800000 0x001000
0x001000 R   0x10
  GNU_PROPERTY   0x0001c8 0x00000000004001c8 0x00000000004001c8 0x000030
0x000030 R   0x8
  GNU_RELRO      0x400000 0x0000000000800000 0x0000000000800000 0x001000
0x001000 R   0x1

But objcopy will take p_align as the maximum page size:

Elf file type is EXEC (Executable file)
Entry point 0x600000
There are 7 program headers, starting at offset 64

Program Headers:
  Type           Offset   VirtAddr           PhysAddr           FileSiz  MemSiz
  Flg Align
  LOAD           0x000000 0x0000000000400000 0x0000000000400000 0x0001f8
0x0001f8 R   0x1000
  LOAD           0x001000 0x0000000000600000 0x0000000000600000 0x000001
0x000001 R E 0x1000
  LOAD           0x002000 0x0000000000800000 0x0000000000800000 0x002000
0x002000 RW  0x1000
  NOTE           0x0001c8 0x00000000004001c8 0x00000000004001c8 0x000030
0x000030 R   0x8
  TLS            0x002000 0x0000000000800000 0x0000000000800000 0x001000
0x001000 R   0x10
  GNU_PROPERTY   0x0001c8 0x00000000004001c8 0x00000000004001c8 0x000030
0x000030 R   0x8
  GNU_RELRO      0x002000 0x0000000000800000 0x0000000000800000 0x001000
0x001000 R   0x1

File offsets are changed.

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