I noticed that in the documentation for jsonURL there is an optional to send an array of strings. Doing this would solve the problem, however it can be inconvenient if two total separate pieces of logic need to share an atlas. This means that there has to be some separate logic which has to know all the json files it needs to load
I never looked at the source directly, maybe it changed? I “solved” my problem by manually editing SpinePlugin.js as explained before. It’s not good since it will be overwritten everytime you update the phaser library