[KaktoR]

That's because the Setup.exe has no [CMDCommand] executed after install process.

[CMDCommands]
@ECHO OFF
SETLOCAL EnableDelayedExpansion EnableExtensions
IF NOT EXIST "{app}\mgstpp_wwise.xtl" GOTO End
CD /D "{app}"
IF EXIST "{app}\wem-unpacker.exe" CALL "{app}\wem-unpacker.exe" "{app}"
"{app}\XTool.exe" decode "{app}\mgstpp_wwise.xtl" "{app}\wwise.tar_extract" "{app}\wwise.tar"
"{app}\7z.exe" x -aoa "{app}\wwise.tar" -o"{app}"
TITLE Repack files, please wait...
SET /A "FileList.Count=2"
SET "FileList[1].Name=00"
SET "FileList[2].Name=01"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\master\0\!FileList[%%i].Name!.inf" (
	CALL "{app}\MGSV_QAR_Tool.exe" "{app}\master\0\!FileList[%%i].Name!.inf" -r
	RD /S /Q "{app}\master\0\!FileList[%%i].Name!"
	DEL /F /S /Q "{app}\master\0\!FileList[%%i].Name!.inf"
	REN "{app}\master\0\!FileList[%%i].Name!.dat" "!FileList[%%i].Name!.tmp"
)
SET /A "FileList.Count=2"
SET "FileList[1].Name=00"
SET "FileList[2].Name=01"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.inf" (
	CALL "{app}\MGSV_QAR_Tool.exe" "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.inf" -r
	RD /S /Q "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!"
	DEL /F /S /Q "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.inf"
	REN "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.dat" "!FileList[%%i].Name!.tmp"
)
SET /A "FileList.Count=11"
SET "FileList[1].Name=chunk0"
SET "FileList[2].Name=chunk1"
SET "FileList[3].Name=chunk2"
SET "FileList[4].Name=chunk3"
SET "FileList[5].Name=chunk4"
SET "FileList[6].Name=data1"
SET "FileList[7].Name=texture0"
SET "FileList[8].Name=texture1"
SET "FileList[9].Name=texture2"
SET "FileList[10].Name=texture3"
SET "FileList[11].Name=texture4"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\master\!FileList[%%i].Name!.inf" (
	CALL "{app}\MGSV_QAR_Tool.exe" "{app}\master\!FileList[%%i].Name!.inf" -r
	RD /S /Q "{app}\master\!FileList[%%i].Name!"
	DEL /F /S /Q "{app}\master\!FileList[%%i].Name!.inf"
	REN "{app}\master\!FileList[%%i].Name!.dat" "!FileList[%%i].Name!.tmp"
)
SET /A "FileList.Count=2"
SET "FileList[1].Name=chunk0"
SET "FileList[2].Name=texture0"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\mgo\!FileList[%%i].Name!.inf" (
	CALL "{app}\MGSV_QAR_Tool.exe" "{app}\mgo\!FileList[%%i].Name!.inf" -r
	RD /S /Q "{app}\mgo\!FileList[%%i].Name!"
	DEL /F /S /Q "{app}\mgo\!FileList[%%i].Name!.inf"
	REN "{app}\mgo\!FileList[%%i].Name!.dat" "!FileList[%%i].Name!.tmp"
)
TITLE Applying patch files, please wait...
SET /A "FileList.Count=2"
SET "FileList[1].Name=00"
SET "FileList[2].Name=01"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\master\0\!FileList[%%i].Name!.tmp" (
	CALL "{app}\xdelta3.exe" -d -s "{app}\master\0\!FileList[%%i].Name!.tmp" "{app}\master\0\!FileList[%%i].Name!.dat.diff" "{app}\master\0\!FileList[%%i].Name!.dat"
	DEL /F /S /Q "{app}\master\0\!FileList[%%i].Name!.tmp"
	DEL /F /S /Q "{app}\master\0\!FileList[%%i].Name!.dat.diff"
)
SET /A "FileList.Count=2"
SET "FileList[1].Name=00"
SET "FileList[2].Name=01"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.tmp" (
	CALL "{app}\xdelta3.exe" -d -s "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.tmp" "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.dat.diff" "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.dat"
	DEL /F /S /Q "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.tmp"
	DEL /F /S /Q "{app}\master\1\MGSVTUPDATEV0110\0\!FileList[%%i].Name!.dat.diff"
)
SET /A "FileList.Count=11"
SET "FileList[1].Name=chunk0"
SET "FileList[2].Name=chunk1"
SET "FileList[3].Name=chunk2"
SET "FileList[4].Name=chunk3"
SET "FileList[5].Name=chunk4"
SET "FileList[6].Name=data1"
SET "FileList[7].Name=texture0"
SET "FileList[8].Name=texture1"
SET "FileList[9].Name=texture2"
SET "FileList[10].Name=texture3"
SET "FileList[11].Name=texture4"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\master\!FileList[%%i].Name!.tmp" (
	CALL "{app}\xdelta3.exe" -d -s "{app}\master\!FileList[%%i].Name!.tmp" "{app}\master\!FileList[%%i].Name!.dat.diff" "{app}\master\!FileList[%%i].Name!.dat"
	DEL /F /S /Q "{app}\master\!FileList[%%i].Name!.tmp"
	DEL /F /S /Q "{app}\master\!FileList[%%i].Name!.dat.diff"
)
SET /A "FileList.Count=2"
SET "FileList[1].Name=chunk0"
SET "FileList[2].Name=texture0"
FOR /L %%i IN (1, 1, !FileList.Count!) DO IF EXIST "{app}\mgo\!FileList[%%i].Name!.tmp" (
	CALL "{app}\xdelta3.exe" -d -s "{app}\mgo\!FileList[%%i].Name!.tmp" "{app}\mgo\!FileList[%%i].Name!.dat.diff" "{app}\mgo\!FileList[%%i].Name!.dat"
	DEL /F /S /Q "{app}\mgo\!FileList[%%i].Name!.tmp"
	DEL /F /S /Q "{app}\mgo\!FileList[%%i].Name!.dat.diff"
)
DEL /F /S /Q "{app}\wem-unpacker.exe"
DEL /F /S /Q "{app}\XTool.exe"
DEL /F /S /Q "{app}\mgstpp_wwise.xtl"
DEL /F /S /Q "{app}\7z.exe"
DEL /F /S /Q "{app}\MGSV_QAR_Tool.exe"
DEL /F /S /Q "{app}\zlib1.dll"
DEL /F /S /Q "{app}\dictionary.txt"
DEL /F /S /Q "{app}\xdelta3.exe"
DEL /F /S /Q "{app}\wwise.tar"
RD /S /Q "{app}\wwise.tar_extract"
TIMEOUT 3
:End
ENDLOCAL
DEL "%~f0"

You can also use this manually, just save it in game folder as batch file and remove

"{app}\"

from the code inside the batch file.

PS: And don't delete the backup folder until everything is done. Check game files after compressing and installation. If they match the checksum then you should delete the backup folder. There is a reason I made it this way.
This game uses encryption on the game files that's why they has to be extracted first, otherwise ratio is bad.