Organizing Face Customizations in Emacs: Custom Faces vs set-face-attribute?

[Kepa]

Hi there!

I've been trying to move some face customizations (default face, org-default 
face, etc.) outside of the area where Emacs automatically manages 
`custom-faces`. My goal was to organize it manually for better control.

Surprisingly for me, Emacs re-creates those customizations in `custom-faces`, 
even without using the customization GUI.
I also have issues with faces like `org-default`, where modifying it affects 
its "heirs", but the text under headlines (which should be `org-default`) 
doesn’t change.

Some other customizations give me errors, using set-face-attribute like if the 
variable wouldn't exist...

What's the best way to configure fonts and emphasis once and for all? Should I 
just stick to `custom-faces` and forget about `set-face-attribute`?

Best regards