I don't know why you got any light at all, either. I don't know why the transistor still works
Because an NPN transistor with its collector and emitter swapped over is still an NPN junction and still works as a transistor but the gain is very much reduced.
"LED's pulsed for say 200% of their 'normal' current at a 50% duty cycle appear brighter than 100% current for 100% duty cycle even though the maths says that it's all the same average current"
That is wrong although it is a common myth. Do your own experiments.
Which one is right?
They both are, it is just they are calculating diffrent things. Having too much base current, even several hundred percent more has no effect on turning a transistor on, it has a slight effect on the time it takes to turn off however.