Just my personal point of views and hope that it will helps.
According to your posting, your child is now 28 month old and so i will now assume that he is 2 years old.
And after taking into consideration that you CLAIMED that your child is having ENOUGH water per day and also MILK...then the only point that i can see where why he is urinating a dark yellow color is because of the followings (allow me to explain it in layman terms):
1. Try take any milk (be it cow, goat or even horse) and boil it! then let it cool down 15 minutes, and then use a spoon to stir the surface of the milk.....you will find a "LAYER" of "Plastic-Like" substances on the top of the MILK.
So, what am i trying to say here is:
When a child is born, their body will produce a natural type of ENZYME in their body to DISSOLVED this layer of plastics and absorb all the nutrients in the MILK.
BUT, unfortunately this type of ENZYME will no longer be produce ONCE the baby is having their first teeth.
So, what am i trying to say here is.....your child is DOING great in terms of DETOXIFYING himself.
Try to give him more water and more wholesome fruits and you shall see a big different cos nowadays MILK formula tends to get more and more complicated and at the same time our body is just not so ready to process too much or to process too fast.
Hope it help, but if u don't get what i really mean u can feel free to ask further and i shall give u a more detail version.
Cheers!