You say “the theory behind it” but there is not a lot of what I’d call theory to setting the base pitch of an analog synthesizer. You’re just choosing the pitch when no control voltage is applied - ie, what note 0V maps to. Then, each volt of CV maps to an increase in pitch of an octave. This is why some people will adjust the pitch knob whilst feeding in a known voltage, eg 2V or 3V, to map 3V to, say, C3 (nicely audible) and then still be in tune down to C0 (which is a much harder note to tune by ear). (If you set them to C3 when they had no CV applied, the only way to go to a lower note would be to apply negative voltage, which isn’t always as easy on many systems).
If they’re both in tune with no voltage applied (or with the same voltage applied), then, if they both track V/Octave, they should be at the same pitch for the same voltages. But they might not be! Reasons they wouldn’t be come down to issues of calibration, and which we might describe as ‘bad tracking’; sometimes this is user-servicable, sometimes not (for instance, on a CEM3340-based VCO I made, it’s a dance that requires a tuner and adjusting two trimpots until the VCO tracks across many octaves). As mentioned earlier, synths can also drift with temperature, which is why analog synths often really do need to literally warm up.
Of course, if you’re only playing the instruments with each other, does it matter if the unmodified base note of the instrument is an actual note in a western scale? Not necessarily! The only time it matters that you’re tuned to a known key, on an analog synthesizer, is when you wish to play with other musicians at the same key. Then you can’t just tune one instrument to another; you’d have to tune them both to a known pitch - eg, tuning to A=440 - rather than just “they both are the same”.
