Are there ways to hide specific confd built in commands from the user? As an example if I don’t want users to be able to use the output-file command, or the cd command, can I hide those?
You can use NACM to hide/deny access to commands and paths. See ConfD UG section “Command authorization” regarding command access. To delete a command for all users, you can use the clispec. See, for example, the clispec(5) man page “confd-light.cli” example.