I have flown on a handful of flights where a prisoner has been transported and actually a few times ex-PBI and each time they have boarded through the jet way like any other passenger, though they did board first, with their wrists covered with a jacket or something to hide the cuffs.

I personally could have cared less, I did not feel any less or more in danger than I normally would, which is to say I generally feel safe aboard aircraft.

Regarding Airline policy, beats me though I imagine that prisoner transport is probably not a reason to be re-booked without penalty.