Thanks for your interest in the Intel Joule board.
To check the voltage level of the PCIe control signals it would be necessary to measure on pins 50, 70 and 72 of the Joule module according to page 6 of the Breakout Board schematic, unfortunately, these pins are not exposed on the Breakout board so it won't be possible to test it this way.
Let me check if this information is available anywhere else, I'll get back to you if I find something.
Thank you for your patience.
In the Joule datasheet it is stated that the PCIe and USB interfaces follow the standards http://www.intel.com/content/dam/support/us/en/documents/joule-products/intel-joule-module-datasheet..., "all I/O signals are 1.8V with the exception of USB and PCIe which adhere to their respective standards."
So it would be necessary to look for this standard on the web to get the information you're looking for regarding PCIe signal voltage.