I'd want to bump this question again. Maybe there are new developments. Saving a deck as an HTML file is neat, however, the web version of Decker struggles with cards where there are multiple animated widgets – it's just super slow. So, I was pondering on the same question as the author – how can I bundle my decks as a single _windows_ executable. I've heard that people release games made in Decker on Steam – so it should be possible.
I experimented a bit with the Enigma Virtual Box – it lets package an executable (Decker) + virtual FS (with a deck file) as a single exe file. But I wasn't entirely successful. It's also a pain to run windows software on wine in MacOS (I know, it's self-inflicted pain, but I have what I have :) ).