Intel uses Synopsys Zebu ASIC emulator, which essentially has Xilinx Ultrascale inside.

I second this, I want details!

I don't work for Intel but I do work for a semiconductor company. While Xilinx FPGAs aren't directly used for prototyping, there are a large number of third party boxes purchased to accelerate hardware simulations and they're chocked full of FPGAs.

That's the more likely explanation. Altera vs Xilinx isn't just the hardware, it's an entirely different toolchain. It would be insane of Intel to demand third parties to move all their technology over to Altera's.