Regardless of setting and intent, she used the rational method - the very definition of rational. Not to mention that, in this setting, magic is treated as a science.
And she doesn't ignore any facts at all. When the evidence points overwhelmingly to the pinkie sense, she gives in and belives in the pinkie sense. Eve while she was testing it, the issue wasn't truly that she believed it wasn't happening, it was that she didn't
know what was truly happening. That's why she strapped pinkie in a machine - she was trying to measure the exact details of what happened when one of Pinkie's twitches went off.
Think of it like the Turing test. A computer set a against the Turing test will be tested by psychiatrists, scientists, and religious figures, to test if it can reason, think like a human, and imitate the 'soul'. The latter of these figures would want nothing less than for a machine to demonstrate the soul. they would likely spend the majority of the testing period fighting the thought for as long as they can. But, three computers to date have passed the test. That means that, despite their initial misgivings, they eventually succumbed to evidence. Twilight did the same. Therefore, her test was no less rational than one established by scientists in our world.