Sadly it breaks intents and doesn't call on local apps despite system settings. Instead it loads the site and only displays an android icon allowing to switch to an app. It's very annoying on slower connections (on the subway for example).
If you're outside the browser, intent resolution proceeds normally. What changes is that if you're in Firefox you need to take an affirmative step to raise the intent instead of going to the web page. To me, that's the sensible default.
Otherwise you end up with nonsense like the following:
1. Clicking on an intent-matching link (e.g. Play Store, Google+, Twitter)
2. Being kicked to the intent-handling app
3. The app deciding not to handle the link (it's some sort of corner case)
4. Being kicked to whatever browser the app picks (often not the one you started with)
Back when devices were sold on the Play Store (not the Google Store), I lost track of the number of times I did this dance when I just wanted to look up something about a Nexus device. The problem was the Play Store app, unsurprisingly, didn't know anything about devices even though it matched Play Store device URLs.