I just played with printing from calibre e-book viewer and regardless of the system setting or book metadata, the default margins were 1.000 inches. As I said, I print PDFs from other programs so never noticed this.
I suspect that changing that behaviour will require a change in calibre's code so perhaps a reports on the
calibre bug report site would be the best path forward.
For what it may be worth, 72 points is equal to 1 inch (computer). On my line gauge/pica pole, 72.27 points equals 1 inch.