The WHO has the political ability to operate at the ministerial and executive level above regular bureaucracy. A technocrat may not care if a senior WHO official arrives on a bicycle, but the WHO does not always deal with technocrats and a meeting planned with a technocrat may turn out to be a meeting with a politician as well or instead.
That's part of why protocols matter for the WHO more than for Médecins Sans Frontières. Protocols also matter more for the WHO because its primary role is at the diplomatic level even during an emergency. During the same emergency, Médecins Sans Frontières primary mission is on the ground delivering services at the endpoint.
But it doesn't matter. If you are part of WHO and arrive at your destination, you aren't going to be greeted on the plane. You're likely going to get off the plane, get in a car, and head to your hotel.
In other words, other people rarely have anything to do with it. Most meetings take place inside a meeting room, not a plane or limo.
The WHO has a unique political capability in regard to reaching consensus on international health policies. It is better equipped to get political commitments from local political leaders when it comes to issues like getting medical supplies across the borders of a dozen countries. In no small part this is because the WHO provides the cover of legitimacy for local political leaders. And with no doubt part of that legitimacy comes from the WHO's ability to project an image of power...it is backed up by UN peace keeping policies. As with diplomacy in general, the WHO travel budget is cheaper than military deployment.