Thomas was doubting that the man he saw before him was Jesus. Not the resurrection. And from that we can assume that Jesus did not look the same as he did before the crucifiction. He wasn’t recognized. So, I say again it doesn’t matter what he looked like. It won’t matter what I looked like once I’m gone. It won’t mean I didn’t exist.
So he believed Christ had risen from the dead, but some body else was pretending to be Him?
That's incorrect. Thomas wasn't present with the other apostles when Jesus first appeared to them. He was doubting the story they told him about Jesus' appearance while he was absent.
So, yes -- I'd say he was doubting the Resurrection.