A long term follow up for others, I eventually realised this was intended behaviour and confirmation is here too https://answers.unrealengine.com/questions/437460/spanish-archive-file-uses-english-translation-text.html
To get around this I made the native culture in the localization export from en to a subset of en (I choose the wonderful Pitcairn Island en-PN) and made the loc for that the exact default that the game exported).
Then we could safely edit the en localization po’s and no worry about breaking localization everywhere else.