Since I'm the one that posted the link (and I listened to a lot of the episodes of the show), I'll post what I heard the stylist had to say. In cosmetology school, stylists are taught that you initially apply the relaxer to the new growth starting ~1/4-1/2" away from the scalp. The smoothing process is what gets the relaxer to the roots. And yes, the body heat will move the relaxer around and the product will eventually get to the scalp, but by doing this you are keeping the product from being on the scalp for less time, which causes less chance for damage to the scalp (as it's the most important part of the hair/head). This is why the stylist is so adamant a/b clients only coming to a professional stylist for this chemical and not doing relaxers at home. (She differentiates b/t the professional and unprofessional stylist in that episode.) She admitted that this is not always avoidable (and that sometimes she is guilty of applying the product to the hair closest to the scalp), but great care is taken to prevent any burning or damage, and she consults with the client to ensure that the right relaxer type for that person's hair and scalp are used, as those are important factors in this process.
I do believe that Shamboosie also mentioned this in his book, which is why he said that if you're going to relax at home for whatever reason, to have a person you trust to do it for you and not to do it yourself.