Yeah, Maxter is on the right track here:
To do intonation modeling with both oscillators, you're going to use four mod slots total (2 for each osc)
Mod Slot 1:
S: Note Num
D: Osc Freq 1
A: 0
Mod Slot 2:
S: Note Num
D: Osc Freq 2
A: 0
Mod Slot 3
S: Seq 1
D: Mod Slot 1
A: Either -1 or +1
Mod Slot 4
S: Seq 2
D: Mod Slot 2
A: Either -1 or +1
(the -1/+1 will determine if going further up keybed gets more flat or sharp.. I found flat to be more common)
In the Gated sequencer, I recommend starting with a defined amount of voices and setting the amount the same in all the virtual voices... +30 for instance. Also, mix one oscillator at a time and check with a tuner... see how many cents sharp or flat the keybed is at the bottom key, and then check the top key... subtract them to figure out what the "total intonation delta" is for the five octave range. If you're happy with that total range, then next step is to center the tuning in the middle of the keybed, or wherever you want it "most perfectly" in tune. Play a middle C, and adjust the fine tune know until that note in the middle of the keybed is perfectly in tune. Apply the same to Oscillator 2.
Next, go back to the gated sequencer where you set all the steps to an equal amount earlier (ie: +30), and now you can give them offsets per voice... maybe keep things in a range between +20 and +40 if you used the example of +30 as your setup starting point... After you've set small/medium offsets for each step, now play, and you'll find you have tons of organic character. Each voice, and each oscillator has intonation / osc scaling to a slightly different degree... which in turn creates natural phasing per voice, and a general intonated character to the tuning of the instrument.
(Note: the +62 value in gated sequencer with -31 fine tune offset is only applicable to the more basic vintage voice modeling without intonation... For this method with intonation, the numbers are going to be different... you have to adjust fine tune to match whatever "centerpoint" you use in the gated seq intonation scaling... if you make the intonation more dramatic, the fine tune will need to be adjusted accordingly to center the sweet spot)