Since Treasury itself notes that the current system works “effectively, with the minimal burden on donors and donees,” this would seem more likely to be an incremental move toward disallowing or substantially burdening the charitable deduction allowance.
As with most things, when you ask for increased government involvement, you can generally count on increased expenses and decreased freedoms.
Umm. If you read the article all the way through, the reason for the proposed rule is that large donors (wealthy and powerful people) won't substantiate their large donations; instead, they, will the help of their lawyers (the tools of their power), are forcing the charities to substantiate their donations to the IRS. The IRS is responding--keeping the wealthy people happy--by forcing the charities to file a new form. Of course, there is outrage against the evil government, and the wealthy get to continue claiming large, fake, unsubstantiated deductions, if they want to.
Don't count on it. The IRS just came out with a simple form complete with with efiling to help people create new 501c3's. If anything, there are going to be more of them.