I believe that there are two distinct questions here. As RBG stated, part of the bonsai process is regular root pruning. This is necessary in order to keep returning the tree to the same pot for years on end. Without root pruning this would not be possible, the tree would lose vigor and die. This continued pruning, roots and foliage, greatly slows a trees growth.
Flowering trees are kept as bonsai and some are very impressive indeed. The thing is though, that they are generally grown out to flowering age/size before their life in a bonsai pot begins. Once they are in a bonsai pot the development phase is ending and the refinement stage begins.
It is a misconception that bonsai are created in bonsai pots, that is seldom the case. Often years of training are carried out before young material is transitioned into a bonsai pot. During this time growth is not restricted, but encouraged. Sometimes this takes place in generously sized containers and sometimes in the ground. Other, more mature, trees are collected from various sources in a more advanced state but still undergo a transition period before they see a bonsai pot.