The language of comparisons

Purists require you to say "different from" rather than "different than", but that's not the issue I find most troubling with comparisons I read in popular websites and blogs.  The error I find so troubling is the comparison of things on different levels of hierarchy.  Let me give you an example.

Joe's car is a different color than my car.

So what's being compared?  The color of Joe's car is being compared to my car.  What was meant here is that the color of Joe's car is different from the color of my car, not different from my car.  Here's how the sentence should be fixed:

Joe's car is a different color than that of my car.

I think a lot of grammarians (whoever they are) would agree this sentence is clearer and all-around better.  Now, let's take it up a level.  Consider this comparison:

The tread on the tires of Joe's car is more worn than that of my car.

See?  I used "that of".  This fixed the problem, didn't it?  No.  There is no "that" meaning tread of my car.  Cars don't have tread.  Cars have tires, and tires have tread.  To fix it properly, you would have to say:

The tread on the tires of Joe's car is more worn than that of those of my car.

But no one says this, or even advocates saying it.  Why?  Do no situations like this ever come up in real life? Yes.

Phys.org reports in article New experiments challenge fundamental understanding of electromagnetism that Quantum Electrodynamics theory (QED) predicts what will happen when an electron orbiting the nucleus collides with a passing particle.  Then it goes on to say,

"The NIST team found that electrons in highly charged helium-like ions that are excited in this fashion give off photons that are noticeably different in color than QED predicts."

Here, phys.org is comparing a noun to a verb, which needs to be fixed this way:

"The NIST team found that electrons in highly charged helium-like ions that are excited in this fashion give off photons that are noticeably different in color than that which QED predicts."

But there's still a problem.  QED doesn't predict a color.  In phys.org's own words, QED predicts "what will happen", i.e. a sequence of events, or events for short.  One of the events predicted by QED is that a photon of a certain color is given off.  This is the color of the photon of the events predicted by QED.  Clear?  QED predicts events which have a photon which has a color.  So then to fix it, the sentence becomes:

The NIST team found that electrons in highly charged helium-like ions that are excited in this fashion give off photons that are noticeably different in color than that of that given off by that which QED predicts.

Alright, I know this is silly.  The point is that comparisons of things on different levels of hierarchy are wrong, and in scientific writing particularly, the sloppy comparisons might lead to misunderstandings of important details.