I actually had to download and try it, to remember the specifics. For this example I just opened up a PHP project.

With refactoring specifically: Komodo supports just "rename class member" and "rename variable" (and "Extract method..." which was constantly unavailable for me).

IntelliJ IDE's support simple renames of members/variables, but more importantly, push/pulling members up/down in a class hierarchy, changing method signatures, moving entire classes into different namespaces.

On top of this, it's little things e.g. the Komodo codeintel doesn't auto-suggest class names if they aren't already imported - you have to import the class (using "use"), and then you can go use it. This is exactly the kind of thing an IDE is supposed to improve - manual steps that can absolutely be automated.