Why is DC voltage biasing applied to a capacitor in distortion pedals
You are correct that in the steady state C3 will have a fixed average potential across it and the actual value, 0 V or 5 V, won't matter. 

The answer may be that bringing up both the inverting and non-inverting inputs together on switch-on - typically by plugging in the jack - minimises switch-on thumps on the output. 


As the 5 V supply rises the pin 3 will rise due to R4.
Meanwhile the left side of C3 will be lifted which will cause the right side to follow, at least for a moment.
The result will be to minimise the difference between the inputs and prevent the output driving hard and fast into saturation.