BaseTools: Set section alignment as zero if its type is Auto

BaseTools: Set section alignment as zero if its type is Auto

REF: https://bugzilla.tianocore.org/show_bug.cgi?id=2881

Currently, the build tool try to read the section alignment
from efi file if the section alignment type is Auto.
If there is no efi generated, the section alignment will
be set to zero. This behavior causes the Makefile to be different
between the full build and the incremental build.

Since the Genffs can auto get the section alignment from
efi file during Genffs procedure, the build tool can just set section
alignment as zero. This change can make the autogen makefile
consistent for the full build and the incremental build.

Signed-off-by: Bob Feng <bob.c.feng@intel.com>
Cc: Liming Gao <gaoliming@byosoft.com.cn>
Cc: Yuwei Chen <yuwei.chen@intel.com>
Reviewed-by: Liming Gao <gaoliming@byosoft.com.cn>
Reviewed-by: Yuwei Chen<yuwei.chen@intel.com>