It seems the best way to do this would be dynamic SQL.

You need to build up a list of columns

DECLARE @sql nvarchar(max);

SELECT @sql =
  STRING_AGG(
    CONCAT(
      '
  a.',
      QUOTENAME(t.TableA),
      '1,
  b.',
      QUOTENAME(t.TableB),
      '2,
  Comparison',
      ROW_NUMBER() OVER (ORDER BY (SELECT 1)),
      ' = CASE WHEN b.',
      QUOTENAME(t.TableA),
      ' = a.',
      QUOTENAME(t.TableB),
      ' THEN CAST(1 AS bit) ELSE CAST(0 AS bit) END'
    ),
    ',
')
FROM Template t
WHERE t.TableA <> 'ID';

SET @sql = '
SELECT
  a.ID,
' + @sql + '
FROM TableA a
JOIN TableB b ON b.ID = a.ID;
`;

PRINT @sql;   -- your friend

EXEC sp_executesql @sql;