pda: transformation between acceptance by empty stack and final states
If I am understanding this correctly, you want to transform a PDA with final state acceptance into one that accepts by empty stack.

First point is, like you mention, when entering an "old" final state to go into a special state where the stack is emptied.

Second point is that we do not want to reach an empty stack at another moment during the computation. Note in that case the old automaton does not accept, but the new one accidentally does! The solution is (indeed) to add a new bottom symbol that can not be removed except at the special state. In that way accidental accepts are avoided. (And this what I understand is the extra part of the construction.)