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I'm building an Astra Telepathica army for my 8th edition project but from a fluff perspective I'm not certain who would have overall command on the battlefield a sister of silence superior or a primaris psyker?

I don't think the Sisters of Silence are in any way related to the Astra Telepathica are they? You put that many blanks near a Psyker and they are going to be clawing their eyes out. The Sisters are a separate Organisation, similar to the Adeptus Custodes.

Edit: Unless you were just talking about Adeptus Sororitas. In that case, no Sororitas would take orders from a Psyker, unless it was an Inquisitor. They absolutely abhor witches, and would probably find an excuse to burn them.

No Sisters of Silence were always under the Astra Telepathica

It also depends on the actual rank. Both the Telepathica's psyker cadres and the Sisters of Silence have actual command structures that aren't represented on the tabletop because both armies' rules are tiny.

And the Adeptus Astra Telepathica doesn't usually deploy the Sisters of Silence and random psykers on the field together; the Sisters' primary duty is to round up untrained psykers and bring them home for sanctioning, while the battle-psyker units are loaned out to support Guard or Inquisition forces. If you had Sisters of Silence and Telepathica psykers in the same army I'd suggest having a third party (probably an Inquisitor) along to make sure they play nice and the bullets/mind-zapping goes to squishing the bad guys instead of each other.