Yes, obviously there are more ways to hide malicious code.
As for the git commit ID, I didn’t see you using it even when it was available though? But perhaps that could be a weakness, if the commit ID used does not match the tag in the repo, that would be a red flag too. That could be worth checking.
Hm, that is a fair point. Perhaps it would make sense to produce a table of checks: indicate which checks each dependency fails/passes, and then colour code them with severity.
Some experimentation on real world code is probably needed. I plan to try this tool on my own projects soon (after I manually verified that your crate match your git code (hah! Bootstrap problem), I already reviewed your code on github and it seemed to do what it claims).