I managed to solve my problem, but not using the Laravel ORM. I think the issue is that the MySQL variables aren't getting initialized when I am using the ORM methods.

I just used the php inbuilt mysql methods and voilà all is well.

Solution:

$query = SELECT hodname, year, month, ptype, pcode, rname, sah, sae, sbe
FROM
(SELECT
(CASE tblhod.hodname
WHEN @curHOD THEN @curHODRow:=@curHODRow+1
ELSE @curHODRow:=1
END) AS seqhodname,
@curHOD:=tblhod.hodname AS hodnamedata,
(CASE WHEN @curHODRow=1 THEN tblhod.hodname
ELSE ''
END) AS hodname,
(CASE tblhod.hodname
WHEN @curHOD THEN CASE tblperiod.year
WHEN @curYear THEN @curYearRow:=@curYearRow+1
ELSE @curYearRow:=1
END
END) AS seqyear,
@curYear:=tblperiod.year AS yeardata, 
(CASE WHEN @curYearRow=1 THEN tblperiod.year
ELSE ''
END) AS year,
(CASE tblhod.hodname
WHEN @curHOD THEN CASE tblperiod.year
WHEN @curYear THEN CASE tblperiod.month
WHEN @curMonth THEN @curMonthRow:=@curMonthRow+1
ELSE @curMonthRow:=1
END
END
END) AS seqmonth,
@curMonth:=tblperiod.month AS monthdata,
(CASE WHEN @curMonthRow=1 THEN tblperiod.month
ELSE ''
END) AS month,
(CASE tblhod.hodname
WHEN @curHOD THEN CASE tblperiod.year
WHEN @curYear THEN CASE tblperiod.month
WHEN @curMonth THEN CASE tblprotype.ptype
WHEN @curPtype THEN @curPtypeRow:=@curPtypeRow+1
ELSE @curPtypeRow:=1
END
END
END
END) AS seqptype,
@curPtype:=tblprotype.ptype AS ptypedata,
(CASE WHEN @curPtypeRow=1 THEN tblprotype.ptype
ELSE ''
END) AS ptype,
(CASE tblhod.hodname
WHEN @curHOD THEN CASE tblperiod.year
WHEN @curYear THEN CASE tblperiod.month
WHEN @curMonth THEN CASE tblprotype.ptype
WHEN @curPtype THEN CASE tblproject.pcode
WHEN @curPcode THEN @curPcodeRow:=@curPcodeRow+1
ELSE @curPcodeRow:=1
END
END
END
END
END) AS seqpcode,
@curPcode:=tblproject.pcode AS pcodedata,
(CASE WHEN @curPcodeRow=1 THEN tblproject.pcode
ELSE ''
END) AS pcode,
tblresource.rname AS rname, SUM(ah) AS sah, SUM(ae) AS sae, SUM(be) AS sbe
FROM `tblallocation`
JOIN tblhod ON tblallocation.hodid = tblhod.hodid
JOIN tblperiod ON tblallocation.periodid = tblperiod.periodid
JOIN tblprotype ON tblallocation.ptid = tblprotype.ptid
JOIN tblproject ON tblallocation.pid = tblproject.pid
JOIN tblresource ON tblallocation.rid = tblresource.rid
JOIN(SELECT @curHODRow:=0, @curHOD:=0,@curYearRow:=0, @curYear:=0, @curMonthRow:=0, @curMonth:=0, @curPtypeRow:=0, @curPtype:=0, @curPcodeRow:=0, @curPcode:=0) v
GROUP BY tblhod.hodname, tblperiod.year, tblperiod.month, tblprotype.ptype, tblproject.pcode, tblresource.rname WITH ROLLUP) AS final;

$con = mysqli_connect('host', 'username', 'password', 'database');
$result = mysqli_query($con, $query);
$data = mysqli_fetch_all($result);

If anyone could point me towards an ORM solution for this would be great!