Yeah manual transfers are fairly common. As Rick says, it depends entirely on that ride’s setup. Some will be aware, some may not (be it through design or modification...). A lot of transfers tend to have a dual locking mechanism, whereby to release the moving portion of track a bolt or stopper gets placed over the open part of the live section. This means if a vehicle is to move into that block it’ll hit the stopper rather than rolling off the end.
Remember that with fairs it’s a very different environment to most fixed parks. The crews will typically work on a small number of attractions (or even just one), and will know exactly how to handle that piece of hardware. There’s generally more of a sense of ownership (especially where it’s a family operation) and the incentive to keep a ride moving. All the while it’s stationary it’s not making you any money. If you break it you’re going to have a very angry showman who’s potentially lost a good chunk of their income on your case, rather than some middle manager filling out an incident report!