The write format for a linked record field is different for Scripting App/Automations compared to Update Automations and the REST API. You need to use an array of objects with record ids.
It isn’t clear what value you are receiving from inputConfig.customLocationID, but it is probably a string, and not an array of of objects. Are you using the search automation action to get the customLocationID? If so, I recommend that you do the search within the script itself, instead of using the search action. That will give you better access to the actual records and their ids.