I agree, one of the issues are tokens with too broad permission sets. However, at the same time, people want general agents which do not have to be unlocked on a repository-by-repository basis. That's why they give them tokens with those access permissions, trusting the LLM blindly.
Your caution is wise, however, in my experience, large parts of the eco-system do not follow such practices. The report is an educational resource, raising awareness that indeed, LLMs can be hijacked to do anything if they have the tokens, and access to untrusted data.
The solution: To dynamically restrict what your agent can and cannot do with that token. That's precisely the approach we've been working on for a while now [1].