How come for two identical overseas business trips, same dates, flights and classes, small new agent B can quote 20% cheaper than bigger agent A, even down to the cancellation charges?

Is it down to agent B being ready to take a lower margin or is it better contact with the airlines or is it just better knowledge of how the system works?

IIRC, psychle used to do that sort of thing, so may well be better equipped to answer!

20% is a pretty big chunk of a difference. If the agent is much smaller, they should have much lower overheads, so could certainly soak up a lower margin. It could also be a bit of a case of them running a loss leader to build a book of business.