Force the join between B and C to take place first, and you change the result:
SELECT *
FROM TABLE_A
LEFT JOIN  TABLE_B
INNER JOIN TABLE_C
 ON TABLE_B.ID =...

Something like this:
SELECT
 [RowIsValid] = CASE
  WHEN AFG = 'Yes' OR [Type] = 'N/A' THEN 1
  WHEN AGF = 'No' OR [Type] = 'Phys' THEN 2
  END,

A simple test harness shows that the method works:

;WITH