SORRY I JUST CANT ANSWER THE QUESTION EXACTLY BUTTTTTTTT I DO HAVE SOME THOUGHTS FWIW
Not knowing the entire circuit and how it functions I cant say for sure, maybe the more electronic (Im more into AC Power Distribution then electronics) gents here or those familiar with a magneto charger can enlighten us??? I do know they have to supply a heavy discharge of DC current for a really strong magnetic field in order to magnetize the mags rotor.
For example, the Capacitors could be used to smooth out and filter the badly pulsed DC wave that results from a diode and half wave rectification??? (But I sorta doubt thats how they are used in your unit, unfiltered pulsing DC is still DC current)
The capacitors (Im sorta thinkin this is how your unit works) could be used to store energy and then provide the capacitor discharge form of sudden released current energy kind of like you seem to be thinking (you metioned capacitor discharge)
If the above is their function, simply to store energy, the more in paralell and/or the higher capacitance rating, the more instantaneous current they could dump to create an even stronger magnetic field !!!!!!!!!!!! HOWEVER you have to match that with the current and capacity the rectifier circuit can produce so once the capacitors are discharged and the rectifier circuit starts to pump current into them the rectifier part of the circuit and the diodes current rating isnt exceeded (cuz theres just toooooo muchhhhhhh capacitance) and you end up frying things!!!!!!!!!
MY BOTTOM LINE BEST "GUESS" IS GONNA BE WHILE THE EXACT CAPACITANCE ISNT NECESSARY AND A TAD MORE WONT HURT,,,,,,,,,IM AFRAID IF THERES TOO MUCH CAPACITANCE YOU MIGHT OVERCURRENT AND DAMAGE THE RECTIFIER CIRCUIT!!!!!!!!
THIS IS NOT AN ANSWER REMEMBER ONLY MY BEST GUESS SO DONT ANYONE HAVE A CALF NOW LOL