I've updated to your latest 1.1 and tested it again. I got the same behavior than previously, when I select a serial port it is set for all projects not just for one.
I also tried to use a specific programmer configuration (preferences->arduino->AVRDude) for each project with an overrided serial port but the serial port used at the end is the one in preferences->arduino->arduino.
This parameter seems to be at the workspace level even if we can set it at the project level isn't it?