Oh don't worry about that, I'm sure the TSA will find some way to get thier tentacles around AmTrak pretty soon.
Not while O'Connor is chief at AmTrak. He is however, getting old. Also, it would be too expensive to force airport-like sterile areas at amtrak station, and there won't be budget allowed for it. There might be marginally more VIPR walk-thrus if congress increases the number of VIPR teams. That would be it.
If they were smart, they'd train and arm certain personnel on the trains, and continue with the bomb sniffing dogs occasionally. The main threats are external along the umpteen thousands of miles of track. As opposed to aircraft, there is quite a different set of threat vectors for land targets like trains.