Heel playing was not comfortable on early organs because of the construction of the pedalboard - it was flat, sometimes the pedals were short, sometimes the range was very wide. Besides, in those days, the main practice instrument for organists was pedal clavichord which also can't really be played using heels. That's why there is a tradition not to use heels in music composed until approximately 19th century (there was certainly some evidence for heel playing in early times as well - perhaps maybe as an exclusion to this tradition).
However, not every organist abides by this rule. Not even every master organist is so strict. That's probably because early performance practice technique were re-discovered in the 1970s together with the first wave of historically inspired organ building.
Some master organists decided to re-learn playing techniques (manual as well as pedal) and some not. Some were mature organists already when this was starting to happen and they learned to use heels and play legato early in their career. To erase all this and start learning from scratch - not everyone is so brave (I was lucky to have studied with two of them - Quentin Faulkner and George Ritchie).
There are organists who advocate for early techniques to be used only on early instruments. They say that wider keys and radiated pedalboards make it impractical to avoid finger and pedal glissandos and substitutions, make it impractical to play with toes only the music of Bach, for example.
Others argue that it would be counterproductive and illogical to learn the same piece in two ways - one to be played on early instruments and one on modern and so they choose early technique on both types.
What do you think?