The actual railroad types need to fill in here, but I think their on-duty hours are always based on counting the number of hours, not on working from x time to x time. So, for labor issues, I don't think it shouldn't make much difference in practice. For record keeping later, maybe.
However when filling out and reading paperwork, like track warrants etc, making sure the correct time is probably more difficult. Not sure if it there won't be an 0200 hour that night or how that works.
And then any overnight trains that are actually scheduled, like Amtrak, they'll be running an hour behind without trying.