Dedicated Transports never use up a force organization slot unless they have a rule that says. In this case, as there is only one dedicated transport available for the Sisters of Silence, the Kharon Pattern Acquisitor, I could find no such rule under its description.
Remember that the Cadre Structure rule (1 HQ/3 non-HQ units) only applies to units with the Company-Cadre rule. Even if the Kharon Pattern Acquisitor was a separate unit, it does not have the Company-Cadre rule.
I really hate Book VII: Inferno.
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