The notation using subscript $i$ is the standard way to express the regression model, although you would also implicitly assume (or explicitly state) that this equation holds over a range of values ---e.g., $i=1,...,n$. When we have different observations/"realisations" of a generic form, we use the subscript notation to specify which of those observations/"realisations". If we do not use the subscript, then it is unclear what we are actually referring to.
In a regression context, the equation $y= \mathbf{x} \boldsymbol{\beta} + \epsilon$ does not really make sense without these subscripts for the observations, because there is no such thing as an "error term" $\epsilon$ that applies in general to all observations. The whole idea of the regression model is that the error terms are the deviations of the observed response values from their conditional expectation, and these deviations are different for different observations. The regression model consists of a stipulated form for the conditional expectation of the response variable and a distribution for the error terms (note the plural --- error terms, not error term).
How the linear regression equation is derived
In order to obtain the model form for the linear regression model, suppose that we are willing to stipulate that the conditional expectation of the response variable is a linear function of the unknown parameters $\boldsymbol{\beta}$ for all the observable values over some sample range. Let's denote this conditional expectation function (called the true regression function) by $u$. This gives us the starting equation:
$$u(\mathbf{x}) \equiv \mathbb{E}(Y_i | \mathbf{X}_i = \mathbf{x}) = \mathbf{x} \boldsymbol{\beta}
\quad \quad \quad \text{for all } i = 1,...,n.$$
Now, the error term for each observation is defined as the deviation of the response value from its conditional expectation ---i.e., for each $i=1,...,n$ we have:
$$\epsilon_i \equiv Y_i - u(\mathbf{x}_i) = Y_i - \mathbf{x}_i \boldsymbol{\beta}.$$
Note that this is a definition of what the error term is measuring. By rearranging this definition we get the standard form of the linear regression model:
$$Y_i = \mathbf{x}_i \boldsymbol{\beta} + \epsilon_i
\quad \quad \quad \text{for all } i = 1,...,n.$$
In order to obtain a regression model, we also need to make some assumption about the distribution of the error terms. The standard assumption is that the error terms are IID random variables with zero mean and a fixed finite variance (often also assumed to be normally distributed). This distributional assumption then gives us the full regression model, but as you can see, the defining equation for the model form follows directly from our definition of what the error terms (again, note the plural) are measuring.
A crucial thing to note here is that the true regression function $u$ is (assumed to be) the same for all the observations. (Consequently, when introducing this function I did not need to put a subscript on the value for the explanatory vector.) This means that we have a single generic true regression function that applies to all the observations. We still need to write our full model form as a set of equations over $i=1,...,n$ because we need to stipulate that this form holds for all the observations. Consequently, while it is not valid to state the model equation generically (since the error terms are different for different observations), there is still a single underlying function that we are trying to estimate.
Okay, so what about estimating the "general form"
In your question, you correctly note that we are interested in the general relationship between the response variable and the explanatory variables. This is encapsulated in the true regression function $u$. By assumption, this function is the same for all the observations, so we are only estimating this one regression function.
When we use the data to estimate the parameter $\boldsymbol{\beta}$ this gives us a corresponding estimator for the true regression function $\hat{u}(\mathbf{x}) = \mathbf{x} \hat{\boldsymbol{\beta}}$, leading to the predicted and residual values defined by:
$$\hat{Y}_i = \hat{u}(\mathbf{x}_i) = \mathbf{x}_i \hat{\boldsymbol{\beta}}
\quad \quad \quad
R_i = Y_i - \hat{u}(\mathbf{x}_i) = Y_i - \mathbf{x}_i \hat{\boldsymbol{\beta}}.$$
Again, you can see that even though we are estimating a single function $u$, this leads to different predicted values and residual values for each of the observations. Consequently, we again see that we need to use subscript $i$ on each of these equations even though they are all based on estimation of the same underlying true regression function.