I get the intent here, but it's a really bad comparison. It's certainly easy to get confused about without base level awareness of finance and accounting things.
The DoD is a government cost center. It doesn't generate revenue. Therefore nothing to tax. Meaning nothing for the IRS to audit.
That's why the federal government has other audit authorities and often contracts independent auditors to help. Those people are auditing department spending and assets related though. This type of audit is not to check if taxes are owed. It's more like making sure the department bank account is correct to keep this simple.