We learned to speak English in a very natural way. We learned through listening and repeating and playfully experimenting with the sounds and the language. Yet when we help others to learn, we force them to remember grammatical formulae and sometimes even a whole new script. Now, I am not a big fan of using phonemic transcription in class. I think that except for the advanced students, it is very confusing not to mention demotivating to see what a pitiful job our alphabet does of representing our spoken language.
My second language is Japanese. A language with three scripts (including the pictoral Kanji) so my objection is not that it is too difficult just that it is not necessary. Like the grammatical formulae, it adds an extra step to the process of producing utterances (or written texts) which slows down the students ability to produce fluently.
I think that phonemic transcriptions and grammatical formulae should be included in teacher trainings but I also think that the teacher need not pass on all information they receive. Instead, they should use that information to find the way that is easiest for the student to absorb.
Keep it simple.