Custom application is an application running in your environment that was created by your organization (or specifically for your organization) and is not likely to be seen in other customers' environments.
Custom App-ID is a custom signature that administrators can create on the firewall to control custom applications (or even common applications where an official App-ID is not yet available)
My understanding these terms are the same. You can create a custom application (additional app-id in Palo local database).
EDIT: @jvalentine has better explanation
There's a lot of instances in the admin guides where a 'custome application' is really an app-id, I can't say I really recall the other way around being brought up though.
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