There is no connection between the waste line and the water inlet unless something has gone very, very wrong. Since there is no connection, there is no path for the waste line to cause any issues with the supply line.
Given that the water in the system is under pressure, I don't see any way that this could even be an issue with the toilet water valve. If the valve leaked, pressurized water would be coming out of it. Air would not be getting in. What is most likely happening here is that air is being introduced somewhere else in your plumbing, then accumulating in the toilet supply line. Finding the source of air might be quite a hunt.