BaseTools: argument genfds-multi-thread create GenSec command issue

BaseTools: argument genfds-multi-thread create GenSec command issue

Issue:
  genfds-multi-thread create makefile before section file generation,
  so it get alignment is zero from empty file. It is incorrect.
solution:
  GenSec get section alignment from input file when the input alignment
  is zero.

Cc: Liming Gao <liming.gao@intel.com>
Cc: Yonghong Zhu <yonghong.zhu@intel.com>
Contributed-under: TianoCore Contribution Agreement 1.1
Signed-off-by: Yunhua Feng <yunhuax.feng@intel.com>
Reviewed-by: Yonghong Zhu <yonghong.zhu@intel.com>