I think the article is a tad misleading here, and I think your first link is going to add to the confusion.
The ability to revoke permissions was built right into the System Settings app, but the ability to access it was hidden from view. Custom roms would usually add a link to it, and apps like AppOps by ColorTiger (your first link) was simply a pointer that would trigger that view to activate (I'm glossing over the root functionality here).
What Google did in 4.4.2 was remove the hidden view from settings. This means that apps like ColorTiger's AppOps will no longer work at all- there is nothing for it to call. The pointer has been dereferenced, if you will.
Apps like LBE (which I share your desire for a newly updated, open source version which doesn't cause bootloops on newer versions of Android), PDroid, and presumably XPrivacy (which I've never heard of, but am looking into now for the inevitable upgrade to 4.4.2 if OmniRom is unable to provide a new solution) work because they replace the functionality that Google removed, not just call something built into Android, but hidden.