Does boiling milk really make the nutrients in it less useful to the body when ingesting it?
The term "denature" is generally used for proteins, and it is true that boiling milk will denature the proteins that are present. Calcium and other such elements would not be "denatured" per se. In fact, I can think of no adverse effect of boiling on the chemical nature of calcium, magnesium, etc. I'm not entirely sure what other minerals and/or nutrients are present in homogenized milk.

As for material being "denatured" during digestion, this is probably an inappropriate term since we generally use the term "metabolized" instead of "denatured". When proteins and other "nutrients" are metabolized, they result in useful products, as opposed to when they are "denatured". So, in summary, I'd say that boiling milk is not the same a metabolizing milk, and I'd say that boiling would likely render milk less "nutritious".