Sorry in advance if i’m not understanding you, but I would have thought it makes perfect sense why they would charge more for flights direct from AMS as opposed to feeder flights to AMS and then onwards. You have to entice people to take the more inconvienent option.
Incidently if you got your fares for the above flights ( LBA-LAX in your example above) from an agent, I would look for a new agent. The BA fare is correct, but that KLM fare is LBA-AMS-MSP-LAX and the same on the way back, so not really like for like, and something I dont think anybody would do. For the comparable to BA fare on KLM (1 stop) the cheapest fare on those specific dates is £1600 in ecomony.