Sometimes we do that because we feel we need to attempt to do everything at once. But in reality, when we play too many things, too many exercises, too many pieces in one practice session, we don't accomplish anything substantial.
If we play through 24 different scales and arpeggios a day just once, it takes considerable amount of time but the progress is very small, if any. This is because in every scale we might make a mistake or two. The wisest thing would be to correct that mistake but sometimes it's difficult to force oneself to stop and perfect that pedal scale or arpeggio.
But there is no other way - we have to perfect what we do, if we want to accomplish something remarkable. So it's better to play only 2 or 4 scales a day but aim for perfection instead of rushing through all of them at once.
Of course, once you master all the pedal scales and arpeggios and want to keep up your already polished technique, then playing through them only once is sufficient. But that's after the real hard work is done, after you master scales in 24 different keys in one octave, two octaves, tonic arpeggios, dominant seventh chord arpeggios, diminished seventh chord arpeggios, scales with double pedals, chromatic scales and so on.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my video Organ Practice Guide.