Do the spellings of cough & rough, pony & bologna bug you, too? English evolves organically, without our permission. Words that look similar but are pronounced differently generally came to the language from different sources and/or at different times, by an organic process that is not controlled by people in smoky board rooms.
In our day, private organizations such as dictionary publishers or the Associated Press do regularly make decisions on how to represent, in English, various foreign or new words, but they do so because today professionals who use the same terms are expected to spell them the same way. Such was not always the case. Of the six documents we have that contain William Shakespeare’s signature, no two are spelled the same.
Before the printing press made books cheap enough for the masses, most people experienced books by listening to someone else reading out loud. In the days before recorded speech or official dictionaries, it wasn’t so easy to figure out the “right” way to pronounce or spell an unfamiliar foreign word. So what you did, when you wrote a book by hand, was represent the sounds, prob’ly w many abbrevs. In medieval times, all the letters in words like “sword” or “walk” or “knight” were pronounced, but over the centuries the pronunciation simplified, while the spelling stayed the same.
Foreign words that came into the English language early (like “noodle” — from the German “nudel”) are spelled the way they sounded to medieval scribes, but the word “strudel” came into English later, when the trend was to preserve the spelling of foreign words. “Balogna sausage” is named for a city in Italy, where the Italian word does not rhyme with “pony.”
Plus, if we mean “nonsense,” we spell it “baloney” — which is much closer to “pony.”
The english word “cough” is an onomatopoeia — that is, a written approximation of the sound of a cough. Just as words like “bark” or “yap” or “woof” are different ways of representing the sound of a dog barking, different spellings, especially back in the days before printed dictionaries, could easily represent different coughs. It just so happened that “cough” became the standard spelling. While the English word “rough” is spelled the same way, it comes from the much older Old English “ruh,” meaning “coarse, shaggy, hairy,” which itself comes from Sanskrit “ruksah” (“rough”). “Though” and “through” both came from Old English words, but over the centuries, nobody was tasked with enforcing that they follow exactly the same path.
About 100 years ago, the American Simplified Spelling Board was founded by Andrew Carnegie, including luminaries such as Mark Twain and Melvil Dewey (of the Dewey Decimal System). US President Theodore Roosevelt was a supporter, and even issued some official presidential documents using simplified spelling. If the spelling reform advocates had succeeded, this is what English would look like today:
bread -> bred
give -> giv
grief -> greef
laugh -> laf
daughter -> dawter
machine -> masheen