I'm not sure I understand what you mean: commas can change the sounds of the word andI see two possibilities: 1. Two cmene differing only in stress are the same. Commas are ignored.
2. Two cmene differing only in stress are different. Commas are ignored unless they change the syllabication of vowels.But the sound are different in that case, and so I think we have different cmene.
The problem with 2 is that syllabication of vowels can be changed without changing the sound of the word, e.g. {malau,is} vs. {mala,uis}.
As to the ,=' rule, I think it's a mistake. Apostrophes are always distinctive, whereas commas are not.I agree. Allowing a comma to be pronounced as an already assigned phonem
Best wishes, Lionel