Commanders provide a logistics bonus to the fleet they are in. However, this bonus only gets applied from the main window. Using the fleet manager does not take account the commander's logistics bonus, so you are still limited to making a fleet with the unmodified faction logistics limit.
A similar bug occurs when launching ships from planetary orbit, or a shipyard or station-- the ejected fleets are limited to the faction logistics limit.
A current workaround is to put the commanded fleet in one hex, and the over-limit ships you want to add in another, and then move the over-limit ships into the commanded fleet. This is, I think, the only way to take advantage of a commander's logistics bonus.
EDIT : This probably has implications for the AI that I haven't analyzed.