Everything is working exactly like I would expect as far as I can see... The skirt speed is properly slowed down by the "first layer speed" setting. For example if you set that to 100% and then to 50%, you can look in the gcode yourself to see that the F-values (i.e. the speed) for the skirt is halved.
The raft is always printed slower by default, so no surprise that it's going to be printing slower than everything else.