flash storage vs PCIe flash storage

Are you deciding between an older macbook pro with a SATA SSD vs. the newer ones with PCIe-based SSDs? That would be the difference. "Flash storage" would refer to a solid state drive that uses a SATA interface (so, think standard 2.5" laptop drive size). The PCIe-based SSD uses PCIe lanes for the interface. This gives them much higher theoretical bandwidth, but it can also easily be the same as a standard SATA SSD. There are a few factors determining how fast they are.

I'll look around for hard data about MacBook Pro PCIe SSD performance. It's not readily available information, and I bet it varies from model to model.

Overall, you will likely not notice a difference in day to day use. It's certainly not a distinguishing factor worth $100+.