Yosef as the unifying root of the shevatim

באפוד הי' אבני שוהם בלבד והוא אבנו של יוסף.

On the eifod (apron of the Kohen Gadol) there were only shoham stones, and this is the stone of Yosef.

The Sefas Emes notes that while the choshen had twelve different stones, the eifod carried only the shoham, which is the stone that represents Yosef among the shevatim.

כי יוסף הוא בחי' זכרון.

For Yosef is the aspect of remembrance (zikaron).

Yosef embodies the quality of zikaron — the ability to keep one's awareness of Hashem present, just as Yosef "remembered" his roots even in the depths of Mitzrayim.

והאבנים היו לזכרון השבטים לפני הבורא ית'.

And the stones served as a remembrance of the shevatim before the Creator, may He be blessed.

The purpose of the stones was to bring Bnei Yisrael to a remembrance before Hashem, so that the entire nation would stand favorably before Him.

ובחושן הי' כל שבט בפרט.

And in the choshen (breastplate) each sheivet was represented individually.

The choshen showed the distinct character of each of the twelve shevatim, each with its own stone and its own particular avodah.

ובאפוד שהוא למעלה על כתפיו.

But in the eifod, which sits higher, upon his shoulders —

The eifod is positioned above, resting on the shoulders of the Kohen Gadol, representing a higher and more all-encompassing level.

הי' כלל השבטים.

— there was the klal (collective whole) of all the shevatim.

At this higher level the shevatim are no longer separate; they are united as one collective body of Bnei Yisrael.

והוא יוסף שהוא שורש כל השבטים ולמעלה מהם כנ"ל:

And this is Yosef, who is the root of all the shevatim and stands above them, as explained.

Yosef, as the aspect of zikaron, is the unifying root that binds all the shevatim together and lifts them to a level higher than their individual identities.

Summary: The single shoham stone of the eifod, which is Yosef's stone, represents the unifying root of all the shevatim — the quality of zikaron that joins the individual tribes (shown separately in the choshen) into one collective whole standing before Hashem.