"FPGA" is a big space, like "processor". There are big server CPUs, and tiny microcontrollers.
The FPGA in that iPhone is the FPGA version of a microcontroller. Those are very popular, as glue logic, and for kludging in emergency fixes after production has already begun. They are also not terribly difficult to program; you hardly even need an HDL, much like you often don't really need a compiler to program a microcontroller.
All the "high level synthesis" pfaff is aimed at the big gigantic $20,000-per-chip FPGAs. Those have mostly been a big fat failure, except for a few big military and cryptocurrency-mining sales. They are wonderful for prototyping ASICs, but that application doesn't sell enough chips to be economically meaningful.
They are very widely used. Some iPhones used an FPGA. iPhone 7 had a small lattice FPGA. https://www.ifixit.com/Teardown/iPhone+7+Teardown/67382