Well, There are many difference and some of them are pointed out by you very well. It also dependent what kind of environment you are in and your requirement.
I have been using angular since angular-2.beta.17
when angular cli was not existed and we have to take the help of many build system and run environment to run the project in anywhere.
Systemjs
building and running:
In some situation where multiple project and frameworks run together, you can not make a AOT build and bootstrap your code into the SPA and run. In system js environement you have to load the scripts one by one and they bootstrap it.
You must have seen this kind of build and loading script in many online tools like codepen, plunker, etc. I think they all uses systemjs loading
There are many other like commonjs
loader, babel
build system, webpack
build system. But now angular cli
is a bullet proof tool with internally use web pack and amber cli to handle everything you want.
Ahead of Time compilation and JIT debugging
As the name suggest AOT do a tree shaking and include everything which is really used in your code and throw away unused codes and compact the code size which can be loaded very fast. But by doing that it looses debugging control and don't give you a nice error message if in case in production you want to see what is wrong.
Same time JIT can point to the line number in typescript file which have the error and make your life super easy to debug while running in dev mode through angular cli.
You can get lot more in angular compiler and there are many tools and games available as well.
one of my favorite is ngrev