Thanks for the insight!
Before coming back here I finally managed to crack it, the game (Battlefleet Gothic 2) can load up multiple Pak files at once provided they have the same name (just in different subfolders inside the pak folder).
Using Unreal I can also load and ‘cook’ assets to be placed inside the custom paks (which can overwrite content from the original pak).
The patch option sounds quite intriguing, I’ll look into it.
I’ve manged to load custom models, images and audio into the game. Blueprint files however are proving more of a challenge as I can’t just create my own, and hex editing the existing files is a minefield. I was recommended the 010 Editor which can apparently do quite advanced stuff with previously in-accessible files like these. (010 Editor - Pro Text/Hex Editor | Edit 200+ Formats | Fast & Powerful | Reverse Engineering)
There’s clearly usable and editable data there, I just don’t have a clue how to edit it without screwing up the file.