Most charitable gifts are a form of tax avoidance (and _all_ of them potentially are if a person's income is such that it makes sense to take advantage of itemized deductions). People get receipts for charitable contributions precisely so they can deduct those amounts from their taxable income. Zuckerberg's plan is of much larger scale, but the fact is that the tax code is set up to encourage charitable contributions by making them non-taxable. The tax code is set up this way, quite understandably, to encourage individuals to make charitable gifts, by creating an extra "bang-for-your-buck" for people who choose to make them.
The linked article seems to suggest that Zuckerberg is trying to take advantage of the system by gaining tax-exempt status while effectively _not_ making charitable gifts, that he is somehow trying to pass everything to the child while taking advantage of tax-exempt status of a charitable organization. I'm skeptical both that his intent is to try to do this, and that there is any scheme that could legally accomplish this.
On a different, but related, note, if I were a parent with $40Bn (or $30Bn, $20Bn, $10Bn, or even $1Bn) I would certainly avoid any plan where the bulk of my estate was to be left to my child. Having that much money is a big responsibility, and it's not something that's likely to add to a person's quality of life. Quite the contrary, it's likely a hindrance, not something I would want to saddle my child with. At most, leave them some large amount ($5M, $10M, $20M, $50M?), something basically guaranteed to make them a wealthy person who doesn't need to worry about money, but hopefully not enough to require that responsible management of their fortune be a main focus of their life. (I realize there are moral implications of having that much money for anyone who has even $10M -- perhaps even $1M -- but when the amounts get astronomical, say to hundreds of millions or more, the moral responsibility really does -- or should -- become almost overwhelming. Not a burden I'd want to put on my child.)