You are very lucky these days if your digital signals are all one logic level for high.
My current design has 1.5V (40R terminated, DDR3 Data and address), 1.5V differential (DDR Clocks), 80 ohm terminated, USB (90 ohm lines), LVDS (100R diff pairs), 1.8V LVCMOS, 2.5V LVCMOS, 3.3V LVCMOS, some 5V doings, some 12Gb/s CML down at the 1V common mode and a few hundred mV signal level, and that is before we get to the nominally 'analogue' doings (All the fast stuff is functionally analogue, if you have to look at eye diagrams then it is analogue design).
FPGA Projects be like that.
The days when all logic had the same reference voltage are LONG GONE, that basically never happens to me on work projects these days and annotating nets with expected voltage is valuable at review time for making checking easier.