1. a fleet having a commander attached to it gives it a bonus to logistics. trying to use the Merge Fleets screen to merge more than the base unmodified max logistics of your empire (i.e. without the commander's bonus logistics) fails to happen. currently you have to move the ships you want to merge onto the commander's fleet to get them to merge.
2. two fleets each with its own commander will not merge regardless of whether doing so will or will not exceed your empire's base unmodified max logistics. I don't know if this is by design (can only have one commander in a fleet) or if this is an oversight. I would have assumed that a basic commander (the one with the bonus to logistics and to movement) could synergy with a promoted-type commander in the same fleet.