I think it's safe to assume that the Team Thor short is non-canon.
As far as we know, nobody knows where Bruce Banner and Thor are by the time of Captain America: Civil War. They've gone AWOL - Secretary of State Ross specifically mentions this in Captain America: Civil War while talking to the Avengers;
"Tell me, Captain, do you know where Thor and Banner are right now? 'Cause you can bet if I misplaced a couple of 30 megaton warheads, there'd be consequences."
Secretary of State Thaddeus Ross, Captain America: Civil War
This obviously goes against what we see in the Team Thor short, with Bruce Banner being in contact with Tony Stark and Thor having Darryl email Steve Rogers for him.
Ultimately, we won't know for sure about the canonicity of Team Thor until Thor: Ragnarok is released, but I feel pretty confident in saying that the third Thor film will "disprove" this short.