You can find what I already answered in the support thread opened on the same question so that it can also be helpful for the community:
Testing window.open() call on the iOS companion app works just as expected on my side, it opens the link in a system browser and not the installed facebook app.
Would it be possible for you to isolate the exact setup you have in a simple project and send it back to me so that I can research the case further? In order to avoid any misunderstanding, may I ask you to also share the steps you perform to observe the problematic behavior?
As a side note, you can check the Facebook Cordova Plugin
in case it can be helpful for you.