For option pricing, we have a formula for the price of an option like the following: $$\Phi(t,S_{t})$$ Where $S_{t}$ is the stock price.
Why not just write in a form of composite function: $$\Phi(S(t))$$ Clearly they are different. But both of them are stochastic processes w.r.t time t. Why should we use the first one? What is the mathematical reason behind that, or the physical meaning under that(I believe it has some).
In Merton's paper, "Theory of Rational Option Pricing," he developed properties of vanilla options (American and European) that relied on strict arbitrage laws and not on any presupposed model for price stochastics.
There are time dependency properties that are based only on these arbitrage laws. For example, Property $(4)$ of the paper states that for two call options with the same underlying asset and same strike, but different times to maturity, the value of the option with the greater time to maturity exceeds the value of the other.
Hence, the value of a call option increases with time to maturity $T$ or equivalently decreases with time $t$. So, there is explicit time dependence due to the "physical" nature of an option.
There are also price dependent properties that are based on arbitrage only. Alongside these properties, Theorem $10$ of the paper proves that if the distribution of returns on the underlying price is independent of the price level, then the value of the option is a convex function of the underlying price.
Thus, an option depends on both time and price as independent variables.