It's not a big deal ....
When the aircraft left the factory, it probably had identical voltage
regulators front and back, that maintained the same voltage.
But, over the decades, you might replace one. And it might be
FAA/PMA approved for your airplane, but it might be of different
manufacture, and maintain slightly different voltage.
I am far too familiar with 12V regulators on aircraft. I know one
brand that likes to maintain 14.3 volts (and is prone to oscillation
on the ammeter). I know another brand that maintains 13.7V and
does not oscillate on the ammeter needle.
Both are legal. Is one better than the other? Probably not. But
if you look at your (external) voltage regulators, I suspect they
are from different manufacturers.
Pro Tip™: go with the single combined box, that is both the
regulator and over-voltage relay. Note that aircraft alternators
(certified, that I have seen) have
external voltage regulators.
Modern automotive alternators have the voltage regulator
inside them. Saves money - no external voltage regulator box
required. No field wire (input).
PS You mentioned something about little batteries. I have a shot
in the dark about that one. Simple scenario: you have a dead
battery on a single, and you hand-prop it. Engine starts. Problem
is, the battery might be dead enough that it cannot energize the
field of the alternator - the voltage is too low. You don't need a lot
of amps to light up an alternator field - just a few volts. I've always
suspected a 9V battery would do it marvellously.
Anyways, with no volts, the result is that the alternator cannot produce
a charge. I suspect your little batteries are for this scenario - to kick-start
the alternator field, when the voltage of the system is near-zero. See
any diodes on the wiring diagram near them? Diodes are like one-way
check valves (most of the time).
Sorry about all this drivel. I used to be an electrical engineer. We
worried about useless shit like this.
PPS If you know about "flashing" a generator - which will charge up
from zero volts - you're probably too old to hold a pilot medical