To test:
Scale with a factor of 3 default cube to use it as smoke domain.
Name its cache as "Erased".
Create an smoke flow plane.
Save untitled.blend.
Bake a smoke simulation.

Create a new .blend.
Add a cube scaled with a factor of 3.
Make it as a smoke domain.
Save as untitled1.blend.
Enable external cache.
Go find "Erased" cache. -> all is ok. smoke is played.
Add a plane next to smoke domain.
Add a particle system.
Bake particle system.
Free all bakes. -> Smoke of untitled.blend can be erased by someone manipulating untitled1.blend.
Move smoke domain. -> "Erased" cache must be rebaked.

Imagine that you have baked a smoke simulation during 16 hours.
You want to add it to a new blend to test a render with that smoke and particles effets you are testing.
So you add a cube, make it as a domain and go find external cache.
You test particles effects. You are satisfied and bake your particle systems and go to sleep.
Someone make you a remark about particle systems. You decide to change some little things.
And press Free all bakes button because you have several particle system to change.
Horror -> you have just free your smoke simulation and lost 16 hours of baking.

I really loved to use external option as an only loading cache option.
I understand that it is needed to export this data to a folder that is not in blendcache folder.

Maybe option for baking could be in scene tab as an external blendcache that could work for particles,cloth,etc with default UI and external cache could still be use to pick up a cache from another .blend.
Maybe operators could be created to bake/free cache of only selected objects or simulation of same type.