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Your explanation seems odd with its focus on the dispensation of the Jews. I was trying to research Chrysostom for this reference and have not been able to track it down. I noticed what John Calvin (who frequently quotes Chrysostom and seems to be a great fan of his) had to say:

Why do the scribes say that Elijah must come first? The gross mistakes which they committed as to the person of Elijah have been pointed out on two or three occasions. Perhaps, too, they cunningly and wickedly endeavored to lessen the authority of Christ by bringing forward Elijah; for as it had been promised that Elijah would come as the forerunner of Messiah, to prepare the way before him, (Malachi 3:1; 4:5,) it was easy to excite a prejudice against Christ, by saying that he came unaccompanied by Elijah. By a trick closely resembling this, the devil enchants the Papists of the present day not to expect the day of judgment till Elijah and Enoch have appeared. It may not usually be conjectured that this expedient was purposely resorted to by the scribes, in order to represent Christ as unworthy of confidence, because he wanted the legitimate badge of the Messiah.

11. Elijah indeed will come first. We have stated elsewhere the origin of that error which prevailed among the Jews. As John the Baptist was to resemble Elijah by restoring the fallen condition of the Church, the prophet Malachi (4:5,6)had even given to him the name of Elijah; and this had been rashly interpreted by the scribes, as if Elijah the Tishbite (1 Kings 17:1) were to return a second time to the world. Christ now declares that every thing which Malachi uttered was true, but that his prediction had been misunderstood and distorted from its true meaning. “The promise,” says he, “that Eliah would come was true, and has been already fulfilled; but the scribes have already rejected Elijah, whose name they idly and falsely plead in opposing me.”

And will restore all things. This does not mean that John the Baptist restored them perfectly, but that he conveyed and handed them over to Christ, who would complete the work which he had begun. Now as the scribes had shamefully rejected John, Christ reminds his disciples that the impostures of such men ought not to give them uneasiness, and that it ought not to be reckoned strange, if, after having rejected the servant, they should, with equal disdain, reject his Master. And that no one might be distressed by a proceeding so strange, our Lord mentions that the Scripture contained predictions of both events, that the Redeemer of the world, and Elijah his forerunner, would be rejected by false and wicked teachers.

This is not to say that Theophylact is wrong but only that Theophylact's and Calvin's interpretations seem to be at odds. There is no indication that Calvin is in anyway referring to Chrysostom's writings. But Calvin often cites Chrysostom and is familiar with his writings. I find Calvin and Theophylact differing views interesting.

Having failed to find any reference in Chrysostom's writings, I was reading Iraeneus writings this morning trying to seek for clues. While it too offers no clues to this particular passage, Iraeneus does talk about the destruction of Jerusalem in the past tense and references Josephus, indicating John the Baptist was "in the spirit of" Elijah. It does not appear from his writing (albeit, it was vague) that he felt Elijah and Enoch would return and all Jews would be saved.

I will admit I might have missed a work that describes all this.