更容易阅读但效率低下（构建三个组、设置标记、concat和排序）：

const inBoth = array1.filter(el1 => array2.some(el2 => el1.INPUT_ID === el2.INPUT_ID))
const minus = (a1, a2) => a1.filter(el1 => a2.every(el2 => el1.INPUT_ID !== el2.INPUT_ID))
const inFirst = minus(array1, array2)
const inSecond = minus(array2, array1)

inBoth.forEach(el => el.ACTIVE_FLAG = 1)
inFirst.forEach(el => el.ACTIVE_FLAG = 3)
inSecond.forEach(el => el.ACTIVE_FLAG = 5)

const res = [].concat(inBoth, inFirst, inSecond)
res.sort( (e1, e2) => e1.INPUT_ID - e2.INPUT_ID)

输入数组必须进行排序（同时遍历两个数组，并确定下一个元素是哪个），这是一种丑陋但有效的方法：

let ix1 = 0, ix2 = 0;
const res = []
while(ix1 < array1.length || ix2 < array2.length){
  const el1 = array1[ix1], el2 = array2[ix2]
  if(!el2 || (el1 && el1.INPUT_ID < el2.INPUT_ID)){
    // element is only in array1
    el1.ACTIVE_FLAG = 3
    res.push(el1)
    ix1++
    continue
  }
  const inBoth = el1 && el1.INPUT_ID === el2.INPUT_ID
  el2.ACTIVE_FLAG = inBoth ? 1 : 5
  res.push(el2)
  ix2++
  inBoth && ix1++
}