When it comes to exchangeable lens cameras (DSLRs/DSLMs), as you increase the number of pixels you very quickly reach a point where you're limited by the optical performance of the lens instead of the sensor. Lots of systems offer a choice between a 24MP and a high pixel count camera (e.g. Nikon Z6/Z7), and you'll find that the high pixel count sibling requires very good lenses to actually achieve a meaningful improvement over 24MP. For these cameras, common wisdom says to stay with 24MP apart from certain niche use cases.

In other words, I wouldn't expect a improvement in capturing actual 48MP pictures in phone cameras, apart perhaps from pixel binning to a smaller size and similar techniques.

Disclaimer: I haven't followed camera tech very closely recently, and I'm not an expert. Take my opinion with a grain of salt.

It might be a 48MP sensor that produces 12MP readout after pixel binning. That's how the sensors on the Sony Xperia 1 work. Does Apple use Sony sensors? I vaguely remember that being a thing.

If image sensor / lens system quality are orthogonal to the final megapixel output, why bother with 48MP output JPEGs? They take up more space, so the practical benefit to smaller files is there.