Answering my own question following further study.
Note first that the regressor may be either fixed or stochastic. The regressor would be fixed if, in an experimental context, the researcher determines values of $x$ and then observes the corresponding values of $y$. If the regressor is fixed, it is not a random variable and therefore there can be no covariance with the disturbance term, covariance being (see here) a relation between random variables. So the question only arises when the regressor is stochastic.
Assuming the regressor is stochastic, how are we to interpret the subscripts in the population regression model? One interpretation is that it refers to a randomly selected unit within the population of interest, with $x_i$, $y_i$ and $\varepsilon_i$ being corresponding values for the same unit. This interpretation seems to be implicit in Wooldridge (A) which describes such a model with subscripts as “the population model for a generic draw from the population”. On this interpretation, $\varepsilon_i$ is a random variable only in the sense that its value depends on which unit is drawn. In this sense, the probability distribution of $\varepsilon_i$ is necessarily the same for each draw. Thus the formula for homoscedasticity is trivially satisfied, while that for no autocorrelation is trivially unsatisfied (the covariance of any variable with itself being its variance which, given random variation in the population, will not be zero).
Another interpretation is that the subscript refers to a sub-population defined by a particular value of the regressor. This interpretation may be found in Gujarati (B). If the population is large and many units share the same $x$-values, then there will be many values of $y$ and $\varepsilon$ for units within a particular sub-population. Hence we can regard $\varepsilon_i$ as a random variable with probability density function $f$ defined by:
$$f(\varepsilon_i) = F_{\varepsilon}(\varepsilon | x = x_i)\quad\quad(1)$$
where $F$ is the joint probability density function of $x$ and $\varepsilon$. (I pass over the possibility that distributions might be discrete, which is somewhat tangential to the question.) Definition (1) allows that the probability density function of $\varepsilon$ may differ between sub-populations. Thus it can support the formulae for homoscedasticity and no autocorrelation, allowing that these properties may or may not be satisfied.
Turning now to the exogeneity assumption, Formulation (2) is inappropriate under either of these interpretations of the subscripts. If the subscript refers to a randomly selected unit, then the condition $\forall i$ implies that, for each particular unit, there is zero covariance between the values of $x$ and $\varepsilon$ for that unit. This makes no sense as those values are not random variables.
If on the other hand the subscript refers to a subpopulation defined by a particular value of $x$, we can allow as explained above that $\varepsilon_i$ is a random variable. But Formulation (2) still makes no sense because $x_i$ is not a random variable.
Formulation (1) is correct. The subscripts, though important for expressing the homoscedasticity and no autocorrelation assumptions, are not needed for expressing exogeneity. Without using the subscripts, Formulation (1) can be related to $F$, the joint probability density function of $x$ and $\epsilon$, as follows:
$$E[x] = \int_{-\infty}^{\infty} xF_x(x) dx \quad\quad(2)$$
$$E[\varepsilon] = \int_{-\infty}^{\infty} \varepsilon F_{\varepsilon}(\varepsilon) d\varepsilon \quad\quad(3)$$
$$E[x\varepsilon] = \int_{-\infty}^{\infty} \int_{-\infty}^{\infty} x\varepsilon F(x,\varepsilon) d\varepsilon\ dx \quad\quad(4)$$
$$Cov(x,\varepsilon) = E[x\varepsilon] – E[x]E[\varepsilon] \quad\quad(5)$$
References
A. Wooldridge, J M (2nd edn 2010) Econometric Analysis of Cross Section and Panel Data p 8
B. Gujarati, D N (3rd edn 2006) Essentials of Econometrics p 136