I believe the Y series has 12 PCIe's. That's enough for four to the SSD, four to Thunderbolt, and enough left for WiFi and Bluetooth.
For whatever reason, Apple equipped the Air's with processors that have a GPU with 48 EU's. Unfortunately, Intel has hung Apple out to dry in terms of an upgrade path for these chips. The only options with equivalent or better GPU's are Iris Plus level parts that have the extra expense of eDRAM. The Mac Mini has gone down the same dead end. Apple needs to switch to inferior graphics, or pony up for a more expensive chip.
Why are the 48 Execution Units such big of a deal? The i5-7300U with HD 620 and 15 W TPD looks like it could be a good choice for a MacBook Air refresh. It only has 24 Execution Units, though.