Basically you are right. Tune the modular and because of the 1V/Oct CV architecture it should track fine. But it gives you also the option to really fine-calibrate this tracking. For example if you have a bad tracking Oscillator you can correct this with the A4 CV calibration. Have a fine middle note C4 with exactly 0.000 Volt and still a very good C8 with 4.107V (instead of exactly 4.000V), for example.
Or, if you want it, go experimental: C4=0.000V and C8=8.000V. This would allow you to have a range of 2 Octaves with the Keyboard notes of one Octave.
Or what about a golden ratio instead of an Octave? C4=0.000V and C5=1.618V!
Or control a Buchla with it. It has 1.2V/Oct. standard.
I do not recommend you to calibrate the A4 or AK to the external CV controlled synth though. Much easier the other way around. And there is also one problem. Since the ratio from one to the next semitone in the AK is always the same and fix (equal temperament) it could be the case that you finetune the AK to the C4 of the Modular Osc and find out that the AK will be totally out of tune at C1 or C7. Which is not the case, it is only bad tracking from the modular Osc. That is why you have the CV calibration.
I hope I could clarify and help.