I don’t know how to read those gerber errors (since I haven’t generated any yet), but glad you wrote the correct fixes to that.
Looking at what you wrote, you mean the PCB view, right? So how to remove the transformation things like the translate at Inkscape?
I think the same thing can be achieved using the xml editor outside Inkscape using Notepadd++ or any code editor and just change the appropriate properties.
Forgot that one, once again, why it is neccesary? 
Was done on purpose since the original one was like that. It is because the sensor isn’t going to be placed on the PCB but the connectors since it is more like “place-replace” part. Following that principle, someone willing to use an ultrasonic sensor only has to worry about where are placed the pin header or holes in case of soldering.