Because different chiffs sound different and affect the stop sound differently, the length of every sample in the organ is different, and the main computer has to be programmed to read the samples in a specific way. If the samples are replaced with other samples of different lengths, the computer won't be able to read them. If Johannus chose to go the easy route and use samples that only included the tone itself, then the samples could be made exactly the same length and the organ could be changed as often as desired. But the very best pipe sound is the result of real time sampling, including the chiff and decay, and Johannus isn't prepared to sacrifice quality for any reason. The second reason is a philosophical one.
Serious artists develop love affairs with their instruments.
They become intimately acquainted with all of the strengths and weaknesses of their personal instruments and they make music as a team the composer, the musician and the instrument. The organ is the most complex instrument in the world, which means that it will take longer to get to know an organ than any other instrument, and the organist is an orchestrator, creating colors and shades of sound unequalled by any other musical artist except the orchestral composer. Not only is that self-defeating for the artist, but it relegates the organ's status to that of a toy a keyboard. If it's more voices you want, almost every organ company, including Johannus, makes a sound module with extra organ samples that can be plugged into virtually any organ or midi keyboard. But Johannus views their organs as serious instruments for the serious artist, and aren't prepared to reduce the credibility of their products simply for the benefit of more gadgetry.