I'd argue JS's behavior makes more sense in this case. Compare:

>>> a = [[1,2,3,4]]
>>> b = [1,2,3,4]
>>> b in a
True
>>> b.append(5)
>>> b in a
False
>>> # so b isn't _actually_ in a!
>>> 
>>> c = [b]
>>> b in c
True
>>> b.append(6)
>>> b in c
True
>>> # but b actually _is_ in c.
>>> # however, before appending `b in a` and `b in c` are the same.

> let a = [[1,2,3,4]]
undefined
> let b = [1,2,3,4]
undefined
> a.includes(b)
false
> b.push(5)
5
> a.includes(b)
false
> // b isn't in a, and we know that from the beginning
undefined
>
> let c = [b]
undefined
> c.includes(b)
true
> b.push(6)
6
> c.includes(b)
true
> // and b _is_ in c, which we also know from the beginning
undefined