I do know that knowledgeable breeders do take stock clones from the bottom of the plant.
I have heard of issues with diploidy which I don`t as yet understand
. (help!)
As far as I do understand the genotype of a plants should be unaffected by the site a clone is taken from.
However I have experienced the way a plant grown from seed will often show diternate (my word- see above) or
symmetrical growth whereas a cutting will show alternate branching. This is surely an expression of phenotype rather than genotype.