PhpStorm PHPDoc type inference: is there a way to manipulate an array and let PhpStorm know its type is same as the original array?

This could be done with PhpStorm's Advanced Meta functionality (PhpStorm uses it for standard array_xxx PHP functions -- have a look here: https://github.com/JetBrains/phpstorm-stubs/blob/master/meta/.phpstorm.meta.php#L64

This does not use PHPDoc though. The extra info (advanced metadata) should be stored in a separate file for PhpStorm eyes only.

Make .phpstorm.meta.php in the project root wit the following content:

<?php

namespace PHPSTORM_META {
    override(\arrayToIdMap(0), type(0));
}

Now the file with your code:

<?php
// Defining used classes and functions

class BaseClassWithGetIdMethod {
    private string $id;

    public function getId(): string
    {
        return $this->id;
    }
}

class Car extends BaseClassWithGetIdMethod {
    public function makeCar(){}
}

class Truck extends BaseClassWithGetIdMethod {
    public function makeTruck(){}
}

function arrayToIdMap(array $models) : array
{
    $result = [];
    foreach ($models as $model) {
        /** @var BaseClassWithGetIdMethod $model **/
        $result[$model->getId()] = $model;
    }
    return $result;
}

// Test code

/** @var Car[] $carList **/
$carList = getCarList();

/** @var Truck[] $truckList **/
$truckList = getTruckList();

$carMap = arrayToIdMap($carList);
//$carMap[0]->

$truckMap = arrayToIdMap($truckList);
//$truckMap[0]->

With the code above PhpStorm provides correct methods:

If it has to be via PHPDoc ... look at generics.

You would need Psalm (or is it PHPStan?) plugin enabled for that (even if you do not use the actual Psalm) as it is how such a support is supplied here. Anyway, both plugins are bundled with PhpStorm and enabled by default. https://www.jetbrains.com/help/phpstorm/using-psalm.html#generics-support

The code:

<?php
// Defining used classes and functions

class BaseClassWithGetIdMethod {
    private string $id;

    public function getId(): string
    {
        return $this->id;
    }
}

class Car extends BaseClassWithGetIdMethod {
    public function makeCar(){}
}

class Truck extends BaseClassWithGetIdMethod {
    public function makeTruck(){}
}

/**
 * @template T
 * @param T $models
 * @return T
 */
function arrayToIdMapZ(array $models) : array
{
    $result = [];
    foreach ($models as $model) {
        /** @var BaseClassWithGetIdMethod $model **/
        $result[$model->getId()] = $model;
    }
    return $result;
}

// Test code

/** @var Car[] $carList **/
$carList = getCarList();

/** @var Truck[] $truckList **/
$truckList = getTruckList();

$carMapZ = arrayToIdMapZ($carList);
$truckMapZ = arrayToIdMapZ($truckList);

$carMapZ[0]->
//$truckMapZ[0]->

That's what I see in my PhpStorm: