Now back to epub correctness. A File in epub format can be validate by an xml validator. If it validates then it should show correctly on your devices! If not then your device is doing something wrong!.
As far as Unicode is concerned. The full unicode does not need to be displayed, nor all glyphs. The devices/readers only should display an alternative that represents
Certainly not a true statement, unless one defines "shows correctly" in a vacuously broad manner. PG/DP HTML/XML authors can and often do write code that only "shows correctly" on at most one browser, and certainly not on epub devices. A common example of this is attempts to implement dropcaps or similar devices. that it can not display that glyph. The devices are supposed to display a "missing glyph" symbol which is unambiguously different than any valid glyph -- and this is certainly not true of epub implementations based on ADE including the Sony Readers who use the valid question mark glyph to also represent the missing glyph symbol.
So the problems you are seeing, do not reflect necessarily a wrong encoding by Calibre, but may be an inability of the device in displaying Unicode!
Could be true, but Calibre displays so many other failure modes, including crashing and hanging forever, as to make Calibre not very usable as an encoding technique to research these issues.