Is this universally the case now? VTEC have tried to charge me £3 because a Great Northern ticket office didn't know how to issue reservations on an obscure weekend day return ticket form Peterborough to York.

The BritRail site does mention that nominal reservation fees are levied for pass holders:

https://www.britrail.net/britrail-seat-reservations

but this could be if you decide to book through them, rather than via the train company directly at the ticket office.