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If by “separate” you mean “on a second die,” there are multiple reasons. First, process technologies for digital circuits are not ideal for analog circuits. So you tune the process differently for each (RF is inherently analog). It’s also typically a much larger node (for technical and cost reasons). And, yes, the RF section creates a lot of noise (inductive, near field, etc.) that will screw up the digital portions of the chip unless you shield them thoroughly. The digital portions of the chip can also screw up the analog portions, which are often quite sensitive!I thought integrating the baseband is the obvious endgame. And why would they retain a separate RF chip? Is there a benefit (less RFI maybe) to keeping the RF chip far away from the processors? Because otherwise, maybe having it as a chiplet integrated in the SoC saves enough power to be interesting.
Integrating it in the same SoC could make sense, but you will also want to keep the analog power supplies and any analog I/O far away from the digital power supplies and I/O; this could create practical problems in a chiplet-style package.
A typical CPU is a mix of analog (RAMs, clock PLLs, I/O drivers) and digital, but these typically have to work at CPU clock rates so we suck it up and work hard to keep things properly isolated. An entire RF chip would create a much more complicated noise profile that would be more difficult to cope with, and my understanding is that these circuits would be difficult to make very efficient and performative if running on a purely-digital tuned process.