"BARREL LENGTH: On shoulder arms and most handguns the distance between the muzzle of the barrel and the face of the breech block or bolt. On revolvers, it is the overall length of the barrel only, including the portion within the frame."
http://www.saami.org/glossary/display.cfm?letter=b
Even if you use your dowel method you won't get 5.4", but don't take my word for it...
This is a pet peeve of mine, I've been in contact with CZ USA, they acknowledged the mistake, promised to fix it for 2014, but apparently didn't. I love CZs, but it really bothers me.