Altering the flash chip would be too obvious. It's a textbook 101 supply chain attack...
Looking at the flash image (dumping it) or chip (x-raying it) would be the first thing anyone would do if they suspected something fishy. A tiny SPI man-in-the-middle chip sandwiched between the PCB fiberglass layers is a lot more discrete and more generic (same MitM chip fiddling with transmitted bytes can attack many different flash platforms, regardless of the sizes/pinouts/footprints of the flash chips).