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.

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.