BaseTools: generate alignment when the FV content come from the filesystem

BaseTools: generate alignment when the FV content come from the filesystem

when the FV contents come from the filesystem instead of from a named FDF
section, the build tool missed to generate alignment for this FV. The fix
is get the alignment value from FV header and use this value to generate
alignment.

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