I believe though I've read that a flow capacitor console can help quickly restore a weapon power level from a beam overload or quickly restore power transfers. There are battery devices (weapons etc) and emergency power to X that can instantly recharge a subsystem ... not sure if that's what you're looking for.
As far as getting more than 125 for a subsytem, you can exceed that value but it doesn't show. As far as I understand it think of it like a hill. The flat section is 100%, the top is 125% the optimum bonus' you can get for exceeding 100%, after 125% the bonus begin to decrease. Its almost like a balancing act trying to keep it at the ideal 125% level, depending on what skills you're using and your playstyle.
From what I gather, they used to help with energy recovery, but now only help with transfers. EPS Flow Regulator consoles have no visible impact on recovery from Full Impulse for instance, but are a huge help when flipping between power presets.