This was an oversight from us. We saw nozzle size as a hardware setting (simmilar to size of the machine), which we thought would not change all that often. This is the main difference between machine settings and ¨normal¨ settings. Changing one of the machine settings results in a ¨new¨ machine, this is why you need to create a new machine definition.
This is changed in the new version (both due to request from you guys as the decision to start shipping with olson hotends).
It is. We´ve spent the past months improving this. There are some drastic changes in the latest version that should resolve (most) of these issues.