On my Trinity a "Program" was essentially a patch, based on one or two waveforms and these went through the ADSR filter and amp settings, and finally through the effects to produce the final patch. It was all self-contained.
So if I get my head around this, Program has been renamed to EXi (and can take the form of any instrument type), and two EXis (two old Programs) now make up a new Program (effectively a mini Combi [duet])?
Right, so, if each EXi is self contained (they have their own ADSR filters, amps and modulation stages etc., like an old Program would have), what architecture does the new Program (aka mini Combi) have? Does that have it's own ADSR filter, amp, modulation, stages etc. too?
I wish Korg would make their mind up what a Program is, lol. On a Trinity a Program was a simple self-contained patch and a Combi was several Programs; meanwhile on the Radias a Program is four timbres (which would class as a combi or ensemble to me); on the Kronos a Program is two EXis (a duet, or mini combi!).
So, does polyphony relate to the number of EXis you use, or the number of Programs you use?
Ok, going back to the first issue, I share the original poster's puzzlement about the restricted sub or the lack of a third oscillator in an AL1 patch (just as I do on the Radias). How come the sub is so restricted? Only triangle or square, and fixed to Osc 1 pitch -12 semitones. The Sub on the MOSS back in 1995 had saw, square, tri and sine, and the pitch (octave, semitone, and detune) was completely independent of osc's 1 and 2 as it had its own pitching page, along with being able to be modulated separately. It was like a third oscillator, and extremely useful too.

^ Dedicated sub-oscillator pitch page

^ Sub-osc pitch modulation sources
And the mixer page allowed independent amp modulations for the sub. You could attach any of the 4 LFOs or 5 EGs to it: http://i53.tinypic.com/52ylmu.jpg
On the Radias (and seemingly Kronos) when I need a third oscillator or a proper independent sub I have to duplicate the patch to a new patch and use it to home the sub and/or osc 3. But then when I tweak the overall sound I have to keep repeating my programming on both patches (like filter settings) to keep them together (osc 1/2/3/sub), as if they were one. Unfortunately this also halves the polyphony as you're using two patches at a time.
At least from the Oasys AL1 manual it appears Osc 2 retains it's own independent modulation of the waveform/pulse-width (like Moss did). On the Radias you can't modulate pulse width or anything on oscillator two, so oscillator two on Radias is like the Moss's old sub-oscillator.