Typically, it doesn’t: by and large, there is just one way to spell any given word. There are three types of exception, though:
I don’t know Kazakh, but I do know that the proliferation of letters with apostrophes in the new proposed alphabet is a mistake.
The Square Hebrew / SimHebrew™ Converter will convert any Square Hebrew text into Roman characters (and back again), with full fidelity with regard to spelling and distinction between seemingly homophonous characters:
As with French, German, Italian, or any other Roman-based language, however, you would have to bear in mind that certain characters have different phonetic values compared with English:
Imagine a Latin text—e.g. the first verse of the Latin Vulgate Bible:
In principio creavit Deus caelum et terram Terra autem erat inanis et vacua et tenebrae super faciem abyssi et spiritus Dei ferebatur super aquas.
Most of us don’t know Latin, but at least we can read it, and guess at the meaning of some words—or look them up.
A straightforward, modern Hebrew rendition would be something like
זעמו של אלוהים יעניש את נשמתך
Yesterday, after ten years of research and development at the University of Waterloo—including two years of collaboration with yours truly and a small collection of other selected translators and editors around the world—I took delivery of a device that will allow me to take real vacations (not the kind pseudo-vacations I usually have, where I furtively try and get some work done as Mrs. Autumn Light yells at me to get off my laptop and join her in seeing the sights or just truly taking it easy on the beach).