I think that vocab lists in books are a combination of the common words and the ones that happen to be used in the verses quoted in the book.
As far as pedagogy words fit into two types of categories; those with or without function (in fact all have function) and those that need to be actively learnt, and those which only need to be recognised.
Those
with function means those who display a particular feature that you are teaching (or have taught). E.g. ἀκολουθεῖν and ὁμοιωθῆναι both require the dative / are constructed with the dative. If that is a feature of the language that you have taught or are teaching, you could bring attention to. Because ἀκολουθεῖν is a more common word, you are likely to introduce it with that word first.
How does function affect frequency? Considering that the accusative more commonly follows a verb than the genitive, dative or prepositional phrases that is to say that it is a common feature in the language.
In effect words like ἀποστελεῖν which takes the most common case (accusative) should get a +1 in frequency because they have a common feature. [In fact they have two common features, the accusative and the infinitive - but don't go grouping this verb + accusative and infinitive construction together with with the accusative and infinitive construction used with verbs of speaking, or you will create confusion. ἀποστελεῖν invokes an infinitive of purpose, while the verbs of speaking only conventionally use an infinitive - just because it is a car doesn't mean you can have any color you like so long as it's black]. For the grammatical point you are teaching, then, certain words have relevance +1's.
Those that need to be learnt actively means two things. First, some example words for each grammatical feature that you introduce. An example that students use to make sense of, or at least recognise, other similar constructions. Second, words that can be mastered for use in conversation and or composition - both of which exercises require master of some skill rather than just knowledge about the word (the usual knowledge about the word is an English word gloss).
Following from that, then, for a student to be able to say that they know a word requires knowledge and skill. Suitable collocations expressing real meaning and the ability to use words within suitable (and correctly formed) grammatical structures.
Another thing about frequent words - a pitfall - is that the words learnt first - at the earliest stages of language acquisiton often only preserve only a beginner's understanding of the word - both phonologically and morphosyntactically. Beginners don't know how to construct phrases, so the common words often remain as strong but independent words - bright points of meaning in the readers mind, rather than part of the flow of a text (or a listening exercise). Having that depth of knowledge / familiarity is both a good thing and bad. It is a great starting point for understanding, but can also obscure the understanding of a whole utterance.
I am only an ESL/EFL teacher (with a hobbyist's knowledge of Greek), and as a teacher, it is very common for me to hear the most simple - and earliest introduced words - pronounced badly, and the most basic tenses used wrongly by intermediate level students - those who are not advanced enough to become self-critical of their language use. It is necessary, for me as a teacher to prompt the students to go back and revisit common words like
ἀκολουθεῖν, because most students tend to stick to their first learnt words with a child-like simplicity that doesn't match their evolving mastery of the language and their developing ability to handle the complexity of the language. Any word that you have a strong one-word gloss for is a good candidate for personally revisiting or for supplementing the reference material with actual usage. What I am saying is that creating blind-spots during the language process is inevitable (and beneficial, because beginners can't handle complexity) and is something that needs to be looked at (corrected) at a later stage of learning, in one or other or all of a few ways.
First, as grammatical structures that an previously introduced word actually does exhibit, but for the sake of creating a manageable simplicity were overlooked, are introduced, then that knowledge can be associated with the familiar word, allowing learners to see what they already know in a new light / from a new perspective. It sounds ideal, but from the reactions I see learners having to it, it is not. Such a dynamic model of language acquisition in a second / foreign language can cause despondency and lack of interest ("Ahh. I thought I knew at least that." "Do I really know anything, if I don't know that." type statements come out). But it depends on the dynamic of the group and their appreciation of your knowledge of the language and skill as a teacher, and their trust in you as a model, even coming down to the compatibility of teacher-student personality types. Second, and to sail a little bit not-so-close-to-the wind, the limited knowledge or skillfulness associate with common words can be brought out in actual usages as time goes by. It is not a bad thing to leave learners with some deficiencies, so long as overall progress is being made. They will (eventually and of themselves) come to a point when single word glosses without grammatical or syntactical information or skill are just not enough. It seems to be okay to speed that awareness up, so long as the teacher (speaking from personal experience and the observation of colleagues) respects that the earliest appreciations of language will always be dear to a learner's heart. An approach like, "Do you remember when you first learnt the alphabet and you said, 'Abou and bulala' for apple and banana." is better than direct correction. The earlier things don't need to be "corrected" as such, because at that early stage of the learning process they were both appropriate and to some degree expected. However, of course it is better if the overall learning process has a built-in self correction for early simplifications such as basing vocabulary learning on concordance search word frequencies as you are - with sound reasons - planning to do.