Comparing an alias to a pointer is like comparing a spoken word to the neurochemistry of the speaker. You know that the speaker can use two different words to refer to the same thing, but what's going on in their brain to make this work is something you don't want to have to think about every time they speak. (If you're programming in assembly or, less so, in C++, you're out of luck there.)
Likewise, PHP *the language* and a given php interpretor are not the same thing, and this post and most of these comments leave that out in the explanation. An alias/reference is a part of the language, a pointer is a part of how the computer makes the reference work. You often have little guarantee that an interpreter will continue working the same way internally.
From a functional point of view the internals of the interpreter *do* matter for optimization, but *don't* matter in terms of the end result of the program. A higher level programming language such as PHP is supposed to try to hide such details from the programmer so that they can write clearer, more manageable code, and do it quickly.
Unfortunately, years ago, using pass-by-reference a lot actually was very useful in terms of optimizing. Fortunately, that ended years ago, so now we no longer need to perform a reference assignment and hope that we remember not to change one variable when the other one is supposed to stay the same. By the time you read this the php that is sending these words to you may be running on a server that uses some kind of new exotic technology for which the word "pointer" no longer accurately describes anything, because the server stores both the program state and instructions intermingled in non-sequential atoms bonded into molecules which work by randomly bouncing off each other at high speeds, thereby exchanging atoms and crossbreeding their instructions and information in such a way as to, in aggregate, successfully run php 5 code. But the code itself will still have references that work the same way they did before, and you will therefore not have to think about whether the machine I just described makes any sense at all.