Due to the nature of the air war, the LF versions of the Merlin, the 66 and the Packard 266 were used for the LFIX and LFXVI. This was because the airwar was much more tactically based and had come down in alt. This occured in late 42-early 43, most likely due to the bombing altitudes of the medium bombers the RAF Spits escorted over France being 18K or so. Once the ground war started things got even lower. There are numerous photos and combat operations where the specialized Spitfire VII had it's extended wings removed and standard wingtips added in the summer of 44 so they too could be used to support the ground war. Imagine flying a pressurized high alt fighter in a low alt war.
The Spitfire IX went through a number of cowling changes. It too had some built with the cut down rear fuselage and bubble canopy but this, like the XVI was very late in the war and not in large numbers. Performance was essentially the same for the LF Spit IX and XVI. Some pilot anecdotes suggest that the Packard was a bit rougher sounding at cruising speeds.
Trying to separate the two birds is just not worth the time as outside of identifying serial numbers, there really isn't a for sure way to tell. Put a Rolls Merlin 66 into a Spitfire XVI and technically it becomes a Spitfire IX. Reverse the engines and the same will make an IX into an XVI. There are restored Spits out there that do this due to restored engine availability.
It's much ado about nothing, and considering ours is a cartoon Spitfire, it's even more of an adventure in silliness trying to make the XVI into something it's not.
Merlin 60 series engines were the first Spit engines to go to two speed two stage superchargers. The Spit VI was the last of the single stage superchargers.
The two stage engines could be adjusted for better performance at different height bands which lead to the HF, F, LF designations on the Spitfire IX for example.
The cropped impeller bit was on the Spitfire Vs that they were trying to improve performance on at lower alt to allow them to compete. "Clipped, Cropped and Clapped" was the pilot's comment on those Spitfire LFVs as they were older airframes with clipped wings and cropped impellers. They were quick down low, but performance really fell off as they got alt.
At lower alts the peformance difference between a modified LFV and a Spitfire LFIX were slight. I believe the previous AH Spitfire Vc that got all the whines by many and is missed by the Spit drivers was based on that performance and not the earlier FV that we have now.
