Does checking the box on your 1040 to contribute to the presidential fund audit proof your return? I have a theory that it helps. The vast majority of audits are based on the DIF score of the return. The DIF score is derived from sample audits of thousands of returns to derive a pattern that is most likely to result in a deficiency. Because it is based on real returns it can be counter intuitive and it takes everything or almost everything into account. For instance, if people from the sample audits who filed on extension using a tax return preparer and claiming very little in charitable deductions tended to underreport their income, your return will get a high DIF score if you also filed on extension using a tax return preparer and claiming very little in charitable deductions.
I have a theory that one of the things that is looked at in determining the DIF score is whether the taxpayer checked the box. It is possible that people in the sample group who checked the box cheated, so checking the box would increase the chance of an audit, but I doubt it. It seems to me that human nature is such that a cheater is not likely to do something designed to promote good government. That supposition is fortified by the fact that in over 50 years of looking at returns, many of which had been audited, I never saw a return that had been subject to audit and on which the taxpayer checked the box. It is true that on most returns the box isn’t checked, so my observation might prove nothing, but combined with my take on human nature I thinking checking the box makes sense.