The whole thing is a bit of a mess really, though as it affects so few people - and as there are few if any guards/RPIs working at that time as well - I suspect its overlooked out of covenience as much as anything else.
For example, there are a couple of trains around 10 past midnight from Durham to Newcastle, which I used in the Autumn when I was living in Newcastle for a few months. I've turned up at Durham at around 10 to midnight and the TVMs have asked if I wanted to travel 'today' or 'tomorrow'. Knowing more than the average bear about rail travel, I knew that I wanted to travel 'today', but it's pretty reasonable to expect that people might buy the wrong ticket at that time. Now, as I've never seen anyone checking tickets at that time, and the barriers are left open, I don't suppose its a problem in practice, but there's clearly potential for confusion.