The plural form here is common, going back to Genesis, where God created the "Heavens" and the earth (heavens being in dual form, so perhaps there were only two or perhaps the dual form was a proto-plural). Post Alexander's conquests, Jewish tradition, infused with the spirit of Hellenism, was obsessed with dissecting, classifying, analyzing, and categorizing everything from the various names and orders of Angels to the number of and kinds of Heavens.
Thus Paul does not say we are seated with God in Heaven, but in the "heavenlies" - eupouranios - here translated as "heavenly places", but "places" is not in the text, being added in English to supply a placeholder noun whereas the Greek only has a plural adjective (plural form of heavenly). Eupouranios appears five times in Ephesians.
One hypothesis is that this was originally a reference to the Heavenly bodies[1], that is, the stars, and thus they were plural. That is to say, the heavenly places were the positions where the stars were set - the heavenly arrangement. So the creation of the "heavens" and the earth might have come from the idea of the stars and the land, rather than the sky and the land.
If this is true, it might lend credence to the idea of gradations -- some sit in one kind of heavenly place while other sit in a different kind of heavenly place. This association of heaven/heavenly body/stars as a possible interpretation of "heavenly places" can be made in many places, but most clearly in the New Testament here:
1 Cor 15.40-4
There are also celestial bodies, and bodies terrestrial: but the glory
of the celestial is one, and the glory of the terrestrial is another.
There is one glory of the sun, and another glory of the moon, and
another glory of the stars: for one star differeth from another star
in glory. So also is the resurrection of the dead. It is sown in
corruption; it is raised in incorruption: It is sown in dishonour; it
is raised in glory: it is sown in weakness; it is raised in power: It
is sown a natural body; it is raised a spiritual body. There is a
natural body, and there is a spiritual body. And so it is written, The
first man Adam was made a living soul; the last Adam was made a
quickening spirit. Howbeit that was not first which is spiritual, but
that which is natural; and afterward that which is spiritual. The
first man is of the earth, earthy: the second man is the Lord from
heaven. As is the earthy, such are they also that are earthy: and as
is the heavenly, such are they also that are heavenly. And as we have
borne the image of the earthy, we shall also bear the image of the
heavenly.
Particularly in Greek myth, there are many traditions of heroes being put into the sky as a constellation or a specific star, and this might be the imagery that's being used here to refer to our spiritual elevation.
The same word is translated as "high places" in Eph 6.12
For we wrestle not against flesh and blood, but against
principalities, against powers, against the rulers of the darkness of
this world, against spiritual wickedness in high places [eupouranios].
Alternately, eupouranios even if it originally comes from the places of the stars, could just be the expression for "the place above, where the heavenly bodies are" and so might not carry the connotation of gradation. Thus we would all be sitting in the same place, but that place would be in the "realm" of the heavenly places. This interpretation is supported by Eph 1.20:
Which he wrought in Christ, when he raised him from the dead, and set
him at his own right hand in the heavenly places (eupouranios),
Thus the plurality could come from different degrees of glorification, or it could just be a linguistic artifact stemming from the idea of the place of elevation being the realm of the stars.
[1] BDAG gives a gloss for eupouranios of being in the sky or heavens as an astronomical phenomenon, celestial, heavenly, celestial bodies.
