Because i and ı are different vowels. If you look closley you'll notice that one has a dot on top and the other without. The one used in makarnayı is dotless. The one with a dot is pronounced the same as the ea in the enlish word beat. The dotless one does not exist in english but sounds like a combination of i and u
I am not sure what the second half of your question is.
Stress is normally on the final syllable, but there are plenty of exceptions. This bit of the Turkish phonology article might be useful for you: https://en.wikipedia.org/wiki/Turkish_phonology#Stress_and_suffixation
The difference between the two vowel sounds sounds is clear to me. But the difference between pasta and the pasta without context is unclear, as in all these cases of accusative, and I can see that a direct object is not always in the accusative - just without any inflection.
Also, I am used to distinguishing in English between Present Simple for regular actions and Present Continuous for what is being done now. Yet we are not given any meaningful examples of this and Present Simple with definite names of foods look strange: you eat many times one and the same apple, orange or fish.