Aggregation of duplicate data
Since you're using 2012+, you have windowing functions available to you which I think make this easier to solve.

Here's my set up.

IF NOT EXISTS
(
    SELECT * 
    FROM 
        sys.tables AS T 
        INNER JOIN 
            sys.schemas AS S 
            ON s.schema_id = t.schema_id
    WHERE 
        S.name ='dbo' AND T.name = 'StagingBenefit'
)
BEGIN
    CREATE TABLE 
        dbo.StagingBenefit
    (
        StagingBenefitSK int identity(1,1) NOT NULL

    ,   EmployeeID int NOT NULL
    ,   BenefitID int NOT NULL

    ,   BenefitProvider char(1) NOT NULL
    ,   Cost int NOT NULL
    ,   FlagA bit NOT NULL
    ,   FlagB bit NOT NULL
    ,   FlagC bit NOT NULL
    ,   BenefitName varchar(30) NULL
    ,   Scenario varchar(30) NOT NULL
    );
END

TRUNCATE TABLE dbo.StagingBenefit;

INSERT INTO
    dbo.StagingBenefit
SELECT
*
FROM
(
    VALUES
        (1,1, 'A', 100, 0, 0, 0, 'Teeth', 'SingleRow')
    ,   (2,2, 'A', 200, 0, 0, 0, 'Teeth', 'DoubleRow, Samesies')
    ,   (2,2, 'A', 222, 0, 0, 0, 'Teeth', 'DoubleRow, Samesies')
    ,   (3,3, 'A', 300, 0, 0, 0, 'Teeth', 'ThreeRow,DoubleFlagged')
    ,   (3,3, 'A', 330, 1, 0, 0, 'Elbow', 'ThreeRow,DoubleFlagged')
    ,   (3,3, 'A', 333, 0, 1, 0, 'Elbow', 'ThreeRow,DoubleFlagged')
    ,   (4,4, 'A', 400, 0, 0, 0, 'Teeth', 'MultipleProviders')
    ,   (4,4, 'A', 440, 0, 0, 0, 'First', 'MultipleProviders')
    ,   (4,4, 'B', 444, 0, 0, 1,    NULL, 'MultipleProviders')
)D
(
    EmployeeID
,   BenefitID

,   BenefitProvider
,   Cost
,   FlagA
,   FlagB
,   FlagC
,   BenefitName
,   Scenario
)
;


I would then look at a query something like this

SELECT DISTINCT
    SB.EmployeeID
,   SB.BenefitID
,   
    CASE 
        WHEN
            MIN(SB.BenefitProvider) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID) 
            &lt;&gt; MAX(SB.BenefitProvider) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID)
            THEN 'Multiple'
        ELSE
            MIN(SB.BenefitProvider) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID) 
        END AS BenefitProvider
    -- SUM this
,   SUM(SB.Cost) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID) As TotalCost
,   CAST(MAX(CAST(SB.FlagA AS int)) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID) AS bit) AS FlagA
,   CAST(MAX(CAST(SB.FlagB AS int)) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID) AS bit) AS FlagB
,   CAST(MAX(CAST(SB.FlagC AS int)) OVER (PARTITION BY SB.EmployeeID, SB.BenefitID) AS bit) AS FlagC
,   MIN(SB.BenefitName) OVER 
    (
        PARTITION BY SB.EmployeeID, SB.BenefitID 
    ) AS FirstBenefit
,   SB.Scenario
FROM
    dbo.StagingBenefit AS SB


Picking through some of the tricks of the query


DISTINCT I feel this is the dirtiest part of it but it solves the problem
MIN/MAX BenefitProvider  - I find the first and last for my window (employee and benefit ids) and if they are different, which I determine via the CASE expression, I use the text Multiple. Otherwise, I just grabbed the minimum but max would work just as well. Heck, I probably could have just skipped the second aggregation call and just made it column name.
MAX Flag - I made this as hard as I could by using a bit data type which you cannot aggregate on so I explicitly convert to an integer and then cast the results of that back to a bit. Same windowing though. Net result is if anywhere my flag is set to true, it'll get preserved across rows
MIN BenefitName - the rule here is to pick the first non-null benefit name. The aggregate function eliminates the NULL and returns the text "First"