alatriste,
i can't really figure out your examples but regarding your Q of the need to increase V speeds when using flex, this is how i understand it.
the reason you can use flex TO is because you have excess runway for that particular TOW at full TO thrust (that's why you use less thrust to save eng life).
also with excess runway, you can use 'increased V speeds procedure' to increase your TOW (you can do this if you are 2nd segment climb limited as opposed to field length limited. this is very often on a 2-eng airplane)
when using flex TO, it's like putting on a smaller engine, as a result your climb performance is compromised. in order, to get your original climb limit weight (at full thrust), you will need to increase your V speeds very similar to 'increased V speeds procedure'.
i hope my explanation helps more than it hurts
SR