You can rename the IRS, you can create a new agency to collect your flat tax or VAT. In the end, it will still, and always be the equivalent of the IRS.
We can rename the Army the Super Fun Happy Team, reorganize their structure, and send them to invade other countries—but in the end, they would sill be the Army.
Since the Civil War, income tax has always been collected by the IRS, or similar (and similarly named) bureaus. Before income taxes, the federal government was mostly funded via tariffs. So you propose replacing the IRS with an empowered Customs and Border Protection Agency? Do you really trust Homeland Security to collect your taxes? Imagine if the IRS has their own navy (with domestic law enforcement powers), law enforcement, immigration, and emergency government operations, and maintains that the Constitution doesn't matter within 100 miles of the nation's borders and coastlines.