What glyphIgo does is explained in the Technical Notes section, at
https://code.google.com/p/glyphigo/
However, I will try to answer:
1) I do not know what Calibre does w.r.t. subsetting, so I cannot tell
2) no, the idea of glyphIgo is checking that an external font (like those shipped with eReaders) can display all the characters contained in a given EPUB (the assumption here is that there are no "embedded" fonts in the eBook).
3) yes, that is the default behavior, but you can consider the entire source code by invoking with the --preserve switch, which will turn off stripping away tags, hence (roughly) just retaining the displayed text.