BaseTools/GenFds: Fix the bug for wrong alignment generate for RAW file

BaseTools/GenFds: Fix the bug for wrong alignment generate for RAW file

When do the multiple raw file support feature, it cause the regression
that the raw file section alignment value was wrongly overridden by the
single raw file. this patch: 1) fix the wrong overridden bug. 2) remove
the duplicate code for combine multiple raw file into one.

Contributed-under: TianoCore Contribution Agreement 1.0
Signed-off-by: Yonghong Zhu <yonghong.zhu@intel.com>
Reviewed-by: Liming Gao <liming.gao@intel.com>