500F supercap charging causes circuit undervoltage (pre-charge)?
Use a wide input range automotive style (robust) DC/DC converter to boost your 12V-24V rail to 28V and then have a further linear or switching regulator to give you clean 24V for the control at all times.  

Alternately I recommend that you have a separate supply for the control if it is always going to be powered from mains.  There is no point having the control at the mercy of the charging PSUs. You can have a redundant pair if you want for that.