In short, everything you emit is a concern, not just IFF. It works with the radar with which it interfaces and is used to provide an accurate ID of an opponent.
In other words, IFF is not an issue. Radar is. Since its used far more frequently to scan airspace. Hence the move to make LPI radars and make them hard to detect. Even there, wide bandwidth RWRs are appearing with significant processing to detect the presence of LPI radars (eg see India's own Varuna ESM system).
The challenge though for the other side is always to range accurately & determine the precise, bearing/azimuth/elevation for accurate firing solutions. Hence, even if the other guy is giving away his location, until & unless you track him with a radar yourself, the average fighter can move so fast that the so called location data you obtained via your ESM a few seconds back, will rapidly decline in terms of accuracy.
The Raptor hence uses its high speed ESM processing to get a rough estimate of where its opponent is by analyzing emitted info. But to generate its own firing solution, it has to go active and shoot out its own pencil beam. This is a quick one time "look, analyze" process as versus a full airspace scan, and is hence considered LPI.
What advanced ground based systems do (IFF/TACAN etc trackers) is use the emitters to build a map of enemy OpFor movement patterns and basing. That is useful but takes time and comprises the entire range of RF bands not just IFF. India has the Divya Drishti program in service for that very thing. The average airborne platform is space/volume constrained and unless specifically designed for the task, does not track such a wide range of surv, fire control, navigational emissions. It focuses on the key things like radar, RF seekers, datalinks, voicecomms, IFF etc with the biggest focus on the first type.
Some older links. Reason I am posting this is so that we see how many actual tracking stations are required for such a task - tracking a wide range of emitters with a decent degree of accuracy. The usual stuff on 1-2 aircraft is simply unable to the job equivalent to what the below do.
DIVYA DRISHTI
Divya Drishti is a joint SI Dte – DRDO programme, with the aim of interception, monitoring, direction finding and analysis (IMDFAS) of communication signals. The system will be installed at various locations on static and mobile stations. All stations will be connected through a satellite communication network. The system caters to the mission of building aircraft flight profile (Mission Analysis).
The DRDO is also developing an all new ESM project in cooperation with the Indian Air Force's Signals Intelligence Directorate, under the name of "Divya Drishti" (Divine Sight). Divya Drishti will field a range of static as well as mobile ESM stations that can "fingerprint" and track multiple airborne targets for mission analysis purposes. The system will be able to intercept a range of radio frequency emissions, whether radar, navigational, communication or electronic countermeasure signals. The various components of the project will be networked via SATCOM links.