Efficiency, output per input, is only relevant for similar inputs. An ICE being more efficient means proportionally lower costs and emissions, but like you said, an electric drivetrain being 90% efficient is less informative than a well-to-wheel comparison.

Similarly, I think it's unhelpful to just expand it to primary energy. What's the efficiency of a wind turbine? In 50 countries already, a 100% efficient ICE would emit more than an EV! The reason for efficiency here was costs and emissions, so compare those.