When charging packs the chances you get a destroyed pack or a charged one are independent of each other, which leads to a single pack turning into both a destroyed and a charged pack or completely disappearing. In macro scale you should get the same amount of packs but it leads to some weird situations where you either duplicate a pack or send it into shadow realm. I tested it with the standard and efficiency packs on the experimental charger.

I'm playing with Space Exploration and a couple qol mods.

(Sorry for delayed reply) Yeah you're totally right, this is a totally valid outcome. I had a look at the options when developing this logic and there was no easy way round probabilistic crafting (that I could see). I justified keeping it the way it is since this mod is pretty late game, and hopefully the infrastructure is on a scale that those shadow realm packs aren't missed, and the inserter or filtering logic can handle either and therefore both outputs anyway.

I'm happy to leave this as "Your're right, but this isnt really an issue" but your're also welcome to submit a PR on the github if you like :)

Hope this is satisfying enough of a response