I'm considering a very similar set-up. So, yes, to me it makes much sense.
Will you use the Flex specifically for your headphone EQ or do you plan on running room EQ too?
If only for headphone EQ, I would leave out the Flex and use EQ APO/PEACE.
For room EQ the Flex is very interesting since you get the option of running Dirac on it too.
There are cheaper solutions to power your HD560s or HD650, but the L50 will do it with plenty of power in reserve. (which is actually not needed but good for peace of mind)