The big difference with most other synths is that with Invader 2 you can 'tune' the main osc independent of the sub. So, by definition, it is not phase locked. The sub behaves more like a simplified 3rd oscillator. For example, in a Mini Moog you have the same phase drifting that causes the same behaviour.
That's simply not the case. The oscillators are free running when the restart button is disabled.
Disabling the 'restart button' doesn't mean that the phases get out if sync instantly. It just stops restarting the oscillators on every note on event.
Yes it applies to all oscillators, but osc1 has a phase offset of half a period to make all oscillators combined sound better.
So, long story short. If you need the exact same phase behaviour for every note, enable the oscillator restart.