I am using the Protected Data Folders to makes sure malware cannot have read access to my document folders and browser data to mitigate the risk of malware stealing my data. Based on my testing I have confirmed that Protected Data Folders also applies to contained applications which are trusted, as Firefox does not work properly in containment with browser cache/cookies/profiles in the protected folders category. These appear to work even though technically I have disabled HIPS. HIPS still works in the background when disabled.
On the other hand, the Protected Files category prevents the files/folders which are defined in the ruleset from being modified or deleted. I personally would like these two features to be merged into one, in which the user can decide what to block without having to navigate between Protected Data Folders for read access and Protected Files for modification and write access, allowing the user to block both or allow access for a specific app in a convenient manner if desired.
So using either protected files or data folders should be able to stop ransomware activity, protected data folders might still allow the ransomware to create it's help files within the folders, but it won't be able to read any of the files in the folder and therefore not be able to modify them, in theory at least. It is important to note that some ransomware also encrypts other files and executables, so I would advise that you only use these features to supplement the containment technology of Comodo and not rely on the HIPS. Even if you block, terminate, and reverse for HIPS, it does not reverse deleted or modified files to their original state at this time.
IMO, the Protected Data Folders is best used for protecting sensitive data which may be stolen by malware. The Protected Files is mainly used to protected critical system resources and is best left alone since containment discards any file system changes anyways, at least with containment enabled.
EDIT: I'm not sure if unknown applications running outside containment are subject to HIPS rulesets when HIPS is disabled, as HIPS still functions in the background when disabled, although I'm assuming that if HIPS is enabled, it would be like the old versions of Comodo before they had sandbox, where a HIPS popup will occur when an unknown application is trying to modify a protected file.