Don’t be silly. Harvard doesn’t double-count applications, It tells you how many total applications it received, and how many people it accepted. In @websensation 's example, that would be 600/10,200, or 5.88%. Generally, its SCEA admission rate would be reported as 10%, and its RD rate would be reported as 5.43% (500/9,200, ignoring the deferred SCEA applicants). Really, the RD rate is 5.00% (500/10,000), but Harvard never reports that, and does not report publicly how many people were deferred from SCEA to RD, so no one can calculate that accurately.
The real numbers, by the way, are something like 7,000 SCEA applications, and 33,000 RD, with 800 SCEA acceptances and 1,200 RD acceptances.
If Harvard wanted to lower its admission rate, it would be simple as pie. Over a decade ago, it started offering some applicants deferred acceptance, forcing them to take a gap year between high school and college (if they wanted to go to Harvard rather than wherever else accepted them). Called the Z-List, it is separate from the normal feature of allowing admitted students to defer enrollment for a year. Harvard has continued to maintain that program, and probably to grow it slightly. I don’t know how many students they accept that way every year, but it’s probably in the 50-100 range. Harvard could simply stop doing that and fill its class with 100 fewer admissions, thereby dropping its admission rate a few more basis points. But they would rather accept more kids, not fewer. Stanford doesn’t do anything similar.