This isn't an official answer, but here goes.
> First, rendering of U+03C3 "Greek small letter sigma". Is it
> allowed and/or encouraged for an application to render this
> code as a final sigma glyph when it occurs word-finally, or
> would this behavior be incorrect?
U+03C3 doesn't take contextual forms. Generally speaking the
standard explicitly mentions contextual forms if shape changes
are to take place. Hebrew is in a similar situation.
> Why is 03C2 not given a compatibility decomposition of
> "<final> 03C3"?
> Assuming that it is legitimate (and indeed should be
> recommended) for 03C3 to be rendered contextually, should
> there be a separate code for "Greek sigma symbol" that
> would be used by mathematicians, etc., when the "normal"
> behavior of the letter sigma is not wanted?
As you point out contextual shaping would cause problems.
There isn't another code AFAIK.
> Section 2.6 "Combining characters" states that "Some specific
> combining characters override the default stacking
> behavior...", [snip] Is there a definitive list of the "specific"
> combining characters that should exhibit such exceptional
> behavior? Or are implementors left to discover the exceptions
> for themselves?
I'm not aware of a definitive list, and I agree one would be
useful. I think Vietnamese and Hebrew are the only other ones.
(That I can think of offhand.) Thai combiners keep a fixed
distance from the base line, so although they stack they don't
(need to) move.
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