BaseTools: Fix corner-cases of --hash feature

BaseTools: Fix corner-cases of --hash feature

BZ: https://bugzilla.tianocore.org/show_bug.cgi?id=1680

Re-order hashing operations so we don't do redundant hashes.

Contributed-under: TianoCore Contribution Agreement 1.1
Signed-off-by: Christian Rodriguez <christian.rodriguez@intel.com>
Cc: Bob Feng <bob.c.feng@intel.com>
Cc: Liming Gao <liming.gao@intel.com>
Cc: Yonghong Zhu <yonghong.zhu@intel.com>
Reviewed-by: Bob Feng <bob.c.feng@intel.com>