Don't worry about it.
You're going to have to get in the habit of tuning it anyway, since the tuning will always fluctuate with ambient temperature. It's hardly ever going to be in tune with the finetune at neutral. That's just how analog is.
All I do is match it to a note on another synth I have - a digital synth I made, so I assume it's in tune. Takes 4 seconds.
As for the scaling, true, if you tune it in one octave, then octaves further away might be a bit off. But what are the odds that the part you've patched in will be played across more than 2 or 3 octaves extensively? If you tune a note in one octave, the note in adjacent octaves will probably be unnoticeably drifted, so you should be fine in most cases.
Last note, don't rely too much on tuners. If you can't notice it being out of tune, then there's no reason to listen to the device telling you it's a couple cents off. Just make music