It is the latter that are shown on the tree. When the F option is not used the output and the cliques reflect only the binary characters. The trees produced have it indicated on each branch the points at which derived character states arise in the characters that define the clique. There is a legend above the tree showing which binary character is involved. Of course if the tree is unrooted you can read the changes as going in either direction.
Different lineages evolve independently.
The ancestral state is not known. Each character has a small chance of being one which evolves so rapidly, or is so thoroughly misinterpreted, that it provides no information on the tree. The true tree has segments which are not so unequal in length that two changes in a long are as easy to envisage as one change in a short segment.