At 27.03 Thunderbird Three is seen without THUNDERBIRD written down its nose-cone.
As Alan is home on Tracy Island on standby, there is no reason for Virgil to be piloting Thunderbird 3.
On Thunderbird 5, John is seen speaking in Gordon's voice with the line, "It looks like we'll be another two hours before we're back in business. In the meantime, International Rescue is non-operational."