"fft" computes a DFT via a FFT algorithm, which just gives you an array of numbers, one complex number per DFT bin. "fftfreq" tells you what frequencies the bins correspond to.
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Regarding changing the length of a sound: A lot of what we subjectively perceive as character of a sound is actually just "encoded" in the transient at the beginning of the sound. Our brain then just remembers that for the duration of the sound and thus it sounds different to us.
So it's important to preserve that transient or it will sound wrong. If it's just beeps then that doesn't matter so much. But for musical instruments and other "real world" sounds it makes a big difference if you cut of the transient. Thanks for coming to my TED talk. ;)
