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i really dont know the full picture but I guess you could do a couple things
I suppose you could go to the other function declaration you did to add taxonomy and just register the model taxonomy in that one
or if you want to just keep what you have for simplicity or whatever
rename this add_custom_taxonomies to addModelTaxonomy()
then use addModelTaxonomy in your init
add_action( 'init', 'addModelTaxonomy');
i suppose its a workaround way but might be simplest for you I don't really want to get too deep into this
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