1. She looks different because she is a different caste of Glukkon. Her development was different from other Glukkons', just as is the case of insects. Remember that that's just one design for Maggie. A different one appears in the Art Book in which her body shape is much more like Sam's.
2. Again, this is just a concept art, and isn't necessarily what the Queen looks like.
3. In the alternative design, Maggie is moved by Kintos.
4. Since she started knocking on death's door by the end of Munch's Oddysee and she has a big part in the story of the Oddworld Quintology, I can only assume she does eventually find replacement lungs, whether they're from a Gabbit or from another Glukkon.
All we really know about Lady Margaret is that she blames Molluck for the destruction of RuptureFarms and the failure to stop Abe from escaping, so upon his discovery, he goes on trial. She also really, really, really hates being called Maggie.
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