How do Calvinists understand the argument that only the Ephesian church were elect in the context of Ephesians?

John Calvin makes a comparison between this verse and Romans 9:11, asserting that the same principal was being described. Thus restricting the scope of application to just the Ephesian church is not warranted.

From Calvin's Commentaries for Ephesians 1:

4. According as he hath chosen us. The foundation and first cause, both of our calling and of all the benefits which we receive from God, is here declared to be his eternal election. If the reason is asked, why God has called us to enjoy the gospel, why he daily bestows upon us so many blessings, why he opens to us the gate of heaven, -- the answer will be constantly found in this principle, that he hath chosen us before the foundation of the world. The very time when the election took place proves it to be free; for what could we have deserved, or what merit did we possess, before the world was made? How childish is the attempt to meet this argument by the following sophism! "We were chosen because we were worthy, and because God foresaw that we would be worthy." We were all lost in Adam; and therefore, had not God, through his own election, rescued us from perishing, there was nothing to be foreseen. The same argument is used in the Epistle to the Romans, where, speaking of Jacob and Esau, he says,

"For the children being not yet born, neither having done any good or evil, that the purpose of God according to election might stand, not of works, but of him that calleth." (Romans 9:11.)

But though they had not yet acted, might a sophist of the Sorbonne reply, God foresaw that they would act. This objection has no force when applied to the depraved natures of men, in whom nothing can be seen but materials for destruction.

In Christ. This is the second proof that the election is free; for if we are chosen in Christ, it is not of ourselves. It is not from a perception of anything that we deserve, but because our heavenly Father has introduced us, through the privilege of adoption, into the body of Christ. In short, the name of Christ excludes all merit, and everything which men have of their own; for when he says that we are chosen in Christ, it follows that in ourselves we are unworthy.

That we should be holy. This is the immediate, but not the chief design; for there is no absurdity in supposing that the same thing may gain two objects. The design of building is, that there should be a house. This is the immediate design, but the convenience of dwelling in it is the ultimate design. It was necessary to mention this in passing; for we shall immediately find that Paul mentions another design, the glory of God. But there is no contradiction here; for the glory of God is the highest end, to which our sanctification is subordinate.

This leads us to conclude, that holiness, purity, and every excellence that is found among men, are the fruit of election; so that once more Paul expressly puts aside every consideration of merit. If God had foreseen in us anything worthy of election, it would have been stated in language the very opposite of what is here employed, and which plainly means that all our holiness and purity of life flow from the election of God. How comes it then that some men are religious, and live in the fear of God, while others give themselves up without reserve to all manner of wickedness? If Paul may be believed, the only reason is, that the latter retain their natural disposition, and the former have been chosen to holiness. The cause, certainly, is not later than the effect. Election, therefore, does not depend on the righteousness of works, of which Paul here declares that it is the cause.

We learn also from these words, that election gives no occasion to licentiousness, or to the blasphemy of wicked men who say, "Let us live in any manner we please; for, if we have been elected, we cannot perish." Paul tells them plainly, that they have no right to separate holiness of life from the grace of election; for

"whom he did predestinate, them he also called, and whom he called, them he also justified." (Romans 8:30.)

The inference, too, which the Catharists, Celestines, and Donatists drew from these words, that we may attain perfection in this life, is without foundation. This is the goal to which the whole course of our life must be directed, and we shall not reach it till we have finished our course. Where are the men who dread and avoid the doctrine of predestination as an inextricable labyrinth, who believe it to be useless and almost dangerous? No doctrine is more useful, provided it be handled in the proper and cautious manner, of which Paul gives us an example, when he presents it as an illustration of the infinite goodness of God, and employs it as an excitement to gratitude. This is the true fountain from which we must draw our knowledge of the divine mercy. If men should evade every other argument, election shuts their mouth, so that they dare not and cannot claim anything for themselves. But let us remember the purpose for which Paul reasons about predestination, lest, by reasoning with any other view, we fall into dangerous errors.

Before him it love. Holiness before God (katenopion autou) is that of a pure conscience; for God is not deceived, as men are, by outward pretense, but looks to faith, or, which means the same thing, the truth of the heart. If we view the word love as applied to God, the meaning will be, that the only reason why he chose us, was his love to men. But I prefer connecting it with the latter part of the verse, as denoting that the perfection of believers consists in love; not that God requires love alone, but that it is an evidence of the fear of God, and of obedience to the whole law.