During the course of the Abyssal War, it was learned it was possible to have a human shrunk down to the size of a fairy and transported on a Kanmusu, just like her normal crew. The process was harmless and let human personnel be transported through high-risk areas safely, and it let human commanders more closely oversee Kanmusu operations.
Boarding procedures, on the other hand, left a lot to be desired, as this admiral is learning as she boards her flagship.
^ But surely they could just hide in their clothes maybe in some pockets or something?
It could be that the properties that allow Kanmusu to combat abyssal ships are part of their bodies and don't extend to their equipment (which is why we can see equipment get destroyed during combat while their actual bodies sustain only superficial damage).
In that case, transporting people externally in pockets or other containers would put them at risk if the ship came under attack.