Phonics is essential, but not sufficient, because of the many parents and contributors to the English language. Our rich vocabulary comes at the expense of consistency, so some look-say is inevitable.
Think of the many simple words that are NOT spelled phonetically:
WAR
TWO
FOUR
MONDAY
DOG
etc.
This doesn’t include the MANY alternate phonetic pronunciations in some of our common words.
BOUGH/PLOUGH
COUGH
DOUGH
ROUGH/TOUGH
etc.
It is well worth the extra memorization, and I would not want to go to sterilizing efforts like some of the Scandinavian countries have to standardize the phonics and pronunciations. We speak, read and write in English. It has the world’s richest vocabulary, because its speakers shamelessly borrow from other countries, perhaps largely due to the centrality of international commerce and colonization during the formation of the modern language. It doesn’t hurt that England venerates her language and created the OED, which the French sneeringly call a museum. The French meant it as an insult, the English do not take it as one.
May I suggest that your phonics education is incomplete as most of the words you list are in fact phonetic. I recommend Spalding method. (spalding.org)
For all those ‘ough’ words, I would teach children that this is the ough phonogram and it has six sounds o, oo uff, off, aw, ow. While pronouncing the sounds I would mimic being struck once for each sound. Little boys quite eat this up and immediately learn to recognize and mimic this fun ninja combination. The sounds are in order of most frequent use and we would have a lesson on those formerly problematic words that are now fun and easy to remember ninja words.