В процентах от общей строки я бы использовал внешний выбор (для удобства чтения), например, так:
SELECT t.[99211] / t.Total AS [99211],
t.[99212] / t.Total AS [99212],
t.[99213] / t.Total AS [99213],
t.[99214] / t.Total AS [99214],
t.[99215] / t.Total AS [99215],
t.Total / t.Total
FROM
(
SELECT pivot_table.MOS,
ISNULL([99211], 0) AS [99211],
ISNULL([99212], 0) AS [99212],
ISNULL([99213], 0) AS [99213],
ISNULL([99214], 0) AS [99214],
ISNULL([99215], 0) AS [99215],
(ISNULL([99211], 0) + ISNULL([99212], 0) + ISNULL([99213], 0) + ISNULL([99214], 0) + ISNULL([99215], 0)) AS Total
FROM
(
SELECT MONTH(c.ClaimServiceDate) AS MOS,
t.[ProcedureCode],
ISNULL(CONVERT(INT, t.NumberofCharges), 0) AS Charges
FROM [EIPODS].[Athena].[claim] c
INNER JOIN [EIPODS].[Athena].[transactions] t
ON c.claimID = t.claimID
WHERE c.ClaimServiceDate
BETWEEN '2016-01-01' AND '2016-09-30'
) t
PIVOT
(
SUM(Charges)
FOR t.[ProcedureCode] IN ([99211], [99212], [99213], [99214], [99215])
) AS pivot_table
) t
ORDER BY t.MOS;
Вам нужно будет отформатировать числа на основе ваших предпочтений, но это должно дать вам% / Total.