It doesnt add 5 to all power levels, it adds 5 to all level of efficiency at commander level.
See the commander skill points you spend maximum of 52 in each shields,weapons,aux,engines well it adds 5 onto that not your power levels.
You must have atleast one point in each to see any benefit and it only boosts any of your power levels which are below 60.
The one point in each prerequisite should theoretically have been fixed and removed with Season One.
Problem is, 5 points in an efficiency skill only gives you an extra 0.83 power if your setting is at 25, which isn't even noticable on its own, since the power numbers are rounded down on the display.