MY THEORY IS..........
Don't forget that the plot was completely different to the Ph today. Jun's original one shot was that 'Pandora' was the heart of the abyss found in chains. It feature Oz, a very angst Gilbert and Reim; under a new name and hes a priest- (you can find this in Volume 8 or chapter 0 @ manga reader)
and so she must have forgotten to change the title when she changed the story
Secondly- could be referred to the Greek myth: Pandora's Box- for instance Oz's curiosity to the pocket watch in chapter 1 led to disaster on his behalf.... or the Abyss, presented as a place with no hope and full of evil- or Jack causing havoc and mayhem YADA YADA - the possibilities are endless
and last but not least Jack created the organization called 'Pandora' in order to gain the Will/Intention of the Abyss... In other words the 'Heart' of the Abyss put the words together and BOOM you've got a title. <and it's fun to say> as i Heart Pandora :D