Checkpoint training would be normal for a lot of situations, but not for regular permanent installation. I would expect any reasonably capable militia group to know how to set up and man a checkpoint too.
I have to agree on the railroad car issue. I have seen several modes of government prisoner transport and to the best of my knowledge, they never use trains. The security problem is the predictability of travel.
The federal system has lots of prisoners who somewhat fit the profile of the "Alex Montel" character from the movie SWAT. That's the guy who says "I'll pay twenty million dollars to whoever gets me the hell out of here!"
Imagine a train car full of guys like that, and some mercenary group, regardless of ideology, quickly figuring out the train schedules. Compare that to the feds current practice of using secure airfields for transporting people like that, and you can figure out that if anyone has any real motivation to rescue prisoner/detainees, trains are just asking to be hijacked.
Compare that to WW2, Wealthy Jews regularly paid bounties to get smuggled out of Europe or to neutral countries like Switzerland and Sweden. Now you did not have swiss Mercs rescuing Jews from the boxcars heading to the concentration camps, but if you look at the money and technology of the day, it would have been extremely difficult. Now compare that to today.
Even civilian groups have access to satellite intel. Even if Google Earth gets turned off, a few people out there have downloaded and saved the few gigs of photo from the most recent updates, in fact it is built into any number of higher end GPS navigation devices now. We have widespread civilian aircraft ownership which means a well funded and trained strike team can get ahead of a train or large convoy once it is spotted on the ground or intel shows they are heading out. In 1939 to 1944, nobody could muster the resources to stop a train in wartime Germany unless it was bombed from the air and then you had the situation of the local population not being particularly motivated to rescue anyone from the train, and the fact that the Nazis had spent close to ten years previously diminishing the accumulations of Jewish wealth so many of the people had a lack of fugitive resources. Europeans and bankers in general have put stopgaps in that over the years, and in European news openly say it is to defy tyrannical governments from attacking accumulated wealth, with the USA being the biggest threat to bank security because US authorities are the only ones who regularly go to foreign network banks with orders to close and seize accounts, although the Brits are picking up the practice pretty quickly.
Then there is other technology involved. Imagine worldwide internet style networks showing videos of the rescue, highly publicizing rewards paid to the rescuers, and finally, the "faces of death" style videos of the execution of surviving guards, train workers and anyone else even remotely involved in the illegal state sponsored hostage taking operation.
Something tells me that a video of some US Marshalls squirming on the pavement still alive from 12G gutshots would have a chilling effect on recruitment into any agency that is just rounding people up and sending them to some sort of concentration camps. Even if such an agency went to foreign recruitment and were recruiting thugs from some backwoods former east bloc republic, I think they might get that message about it not being a really good idea to pull any of that holocaust stuff in this country ever.
I know there are some deep underground neo-nazi types who think that they can take over a major government again and restart the holocaust, maybe even take over the US and nuke Israel, but they need to understand that the Sampson option is no longer limited to short range targets.