I think you avoid all the CROSS APPLYs, as below.

As written the code just ignores anything beyond 24 hrs, but if you needed to, you could add a check for that.

SELECT

StartTime, EndTime,

CONVERT(varchar(8), DATEADD(SECOND, DATEDIFF(SECOND, StartTime, EndTime)

- CASE WHEN DATEPART(NANOSECOND, StartTime) > DATEPART(NANOSECOND, EndTime) THEN 1 ELSE 0 END, 0), 108) +

'.' + RIGHT(REPLICATE('0', 7) +

CAST(((CASE WHEN DATEPART(NANOSECOND, StartTime) > DATEPART(NANOSECOND, EndTime) THEN 1000000000 ELSE 0 END +

DATEPART(NANOSECOND, EndTime) - DATEPART(NANOSECOND, StartTime)) / 100) AS varchar(7)), 7) AS TimeDiff

FROM SourceTable

ORDER BY ID