gistfile1.js

function test() {
  let a = 4;
  if (true) {
    const x = 1;
    var y = 2;
    let a = 3;

    a = x + y;
  }

  console.log(a);
  if (typeof a === "undefined") {
    console.log('a should change to the top-level one', a);
  }

  if (typeof x === "undefined") {
    console.log('should stay as x in the typeof');
  }
}

// becomes
function test() {
  var $__0;
  var $__1;
  var $__2;
  $__0 = 4;
  if (true) {
    $__1 = 1;
    var y = 2;
    $__2 = 3;
    $__2 = $__1 + y;
  }
  console.log($__0);
  if (typeof $__0 === "undefined") {
    console.log('a should change to the top-level one', $__0);
  }
  if (typeof x === "undefined") {
    console.log('should stay as x in the typeof');
  }
}

A cleaner output might look like:

// becomes
function test() {
  var a = 4;
  if (true) {
    var $__1 = 1;
    var y = 2;
    var $__2 = 3;
    $__2 = $__1 + y;
  }
  console.log(a);
  if (typeof a === "undefined") {
    console.log('a should change to the top-level one', a);
  }
  if (typeof x === "undefined") {
    console.log('should stay as x in the typeof');
  }
}

Or rename the vars to something that has the original name in to make it easier to reason about

function test() {
  var a = 4;
  if (true) {
    var $__x = 1;
    var y = 2;
    var $__a = 3;
    $__a = $__x + y;
  }
  console.log(a);
  if (typeof a === "undefined") {
    console.log('a should change to the top-level one', a);
  }
  if (typeof x === "undefined") {
    console.log('should stay as x in the typeof');
  }
}

I'm not sure how safe a renaming like that would be. We could do a more sophisticated temp var scheme at some later point. Don't let that block you.