The subject is a verb.
When you have a verb of location or motion, and an adverbial phrase of time or place, you can optionally emphasise the adverbial phrase by putting it first, then the verb, then the subject:
The book was on the table => On the table was the book.
The verb comes after "by" => After "by" comes the verb.
John lay on the bed => On the bed lay John.
Alice came next => Next came Alice.
The farmer came round the corner => Round the corner came the farmer.
The subject is still the subject, but this makes the adverbial the topic of the sentence.
With an indefinite subject, you can optionally use the presentative there; this is a slightly different construction, but there is still not the subject:
A man stood next to the window => Next to the window [there] stood a man.
So you can say After "by" comes a verb or After "by" there comes a verb. But you cannot use dummy it in this construction, because (unlike there) it would take the subject role, and there would in most cases be no grammatical role for the original subject.