I understand the reason behind issue #3 now. It has to do with how EMF spits out elements when there is node inheritance going on. For example if in your ecore model you have
NodeA -> NodeB (extends node B)
a
b
NodeB (abstract = true)
x
y
the output XML becomes:
<A>
<x/>
<y/>
<a/>
<b/>
</A>
instead of
<A>
<a/>
<b/>
<x/>
<y/>
</A>
Looking into EMF docs to see if there is any setting that may help here. For now please disable schema validation when testing in Eclipse env.