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[0]
, 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.