Connecting 1.8V USB and PCIe to 3.3V system
So, PCIe is not 3.3V signalling at all; it's a differential, AC-coupled bus with some 0.5 Vpp or less voltage swing. There's no problem here.
USB2 Low and Full Speed indeed does signalling with a voltage higher than 1.8 V, but high speed doesn't, and I think you can negotiate that you do high-speed without having to support the high speed IO.
While I feel (don't actually know) that building a device that's high-speed-only isn't quite USB-specification-compatible, that doesn't matter too much for Google: their target market for the USB-connected variant clearly is embedded devices, i.e. devices where they do the Google-typical thing of not actually quite 100% implementing something so that it works out of the box, but shooting themselves in the foot by requiring the other end to employ a quirk, and having problems with that for years. In this case, it's reasonable (but bad style, in my humble opinion) to assume the host can be forced into high-speed mode.