Well, Marco's morph may not have affected the Animorphs/Helmacrons inside him, but it did destroy the rabies bacteria that were also in his body at the time. Which seems to imply that the morphing technology has some ability to distinguish between what should or shouldn't be altered by the morph. The way I see it, the whole technology is fundamentally thought-controlled in the first place, right? So, if the tech has access to your mind, maybe it can read your thoughts and know what is or isn't a necessary component of your body that needs to be preserved. It would be subconscious, maybe reliant on some subliminal self-image, so you couldn't 'trick' the technology and give yourself a different haircut or something. And it makes sense that the Andalites would program the technology this way, so as to preserve the shortened hair of unschweet (wouldn't want those dishonored soldiers getting a free pass, would you?).
There's plenty of other examples of this. Rachel's haircut in book #2, various Andalites keeping their scars despite being morph-capable, the fact that Rachel has pierced ears even after many morphs.
As for the 'large morphs' thing, I've always assumed that antimatter could also be extruded into z-space. Whereas a smaller morph extrudes 'positive' matter, a larger morph would basically extrude 'negative' matter instead. No need for extra mass floating around out there waiting to be used by a large morph.
