Hey Will, thanks!
The paper is from quite a few years ago now and the reference is for a subset of gittuf's threat model, specifically the metadata manipulation / reference state attacks. The paper talks about MITM as one way to carry out a ref state attack, but if you're communicating with a compromised repository, you can be a victim of such an attack even if you're using authenticated transport and using signed commits / tags that you have a way of verifying.
We do have a threat model for gittuf that we've been meaning to add [0] to the design doc. I'll try and get that done today. It should probably be in there before we tag our alpha release. :)