It make sense. We will try to choose what is better for gameplay. You see- Fallen Brothers and sisters are strong opponents, and may be it will be better to leave them as they is? Just for your own safety?
Thing is, they're set up in the GECK as Raiders, with RaiderFaction and "Helps Allies". They're also described on the FWE homepage as "captians among the malicious hordes". Yet, you can enter a Raider Den, kill all the regular raiders right in front of them and get no reaction at all. They you casually walk up behind them, blow their heads off before they can even draw their gun and leave with Outcast Armor and a decent weapon. That seems utterly pointless.
As for the "Intense Training" issue, I think the problem is that although you choose to take "intense training 1", the game lists you as having one rank of the vanilla Intense Training....so you are never recorded as having "Intense Training 1" and the game thinks it should still be available.