If you have a 3KVA transformer constructed with 2 secondary coils which are 'field wired' in parallel, the secondary protection would be for the _parallel_ coils, not for the individual coils.
This is what I meant by a clear distinction that does not make a practical difference. Yes, if you have two coils in parallel versus a single coil, you have a potential failure mode where one of the parallel coils gets disconnected and the other coil gets overloaded. However secondary protection _if required_ would not protect from this failure mode. In cases where secondary protection is required, it is for the _entire_ secondary, not portions of the secondary.
Now if you had a 20A secondary consisting of two parallel 10A coils, with separate 10A OCPD in each coil that would be a different story, but NEC doesn't require this.
-Jon