Peak to peak levels are also always configurable (that's the drive strength part of the link training I mentioned).
But I think you're missing my larger point which is, all PCIe devices (including motherboards with redrivers, etc.) must support linking up at the PCIe 1.0 spec, or they will not work at all. It doesn't matter if the incompatibility is electrical swing, speed, tiny leprechaun interference, or anything else. Because when first powered on, the PCIe spec (I just looked at 4.0 but I'm sure 5.0 didn't change anything here) says that everything links up as if it's a PCIe 1.0 device just so that they can easily communicate without having to worry much about signal integrity. Then, once the devices can talk (slowly) to each other, they advertise what speeds they support, and will possibly adjust electrical parameters (such as peak to peak voltage) to make sure the bus can support the signal integrity of the high speed link, and only then will they switch to a faster speed. If a device cannot do this, then it's not compliant with the spec, and probably won't work at all.