This paper can be boiled down to:
If you have malware on your CI machine it can infect the artifacts it creates.
In this paper the malware was a strip trojan, but it could have been just as well a normal piece of malware which starts a service and then waits for the final artifact to be generated after which it infects it.
Rebuilding strip from clean source doesn't clear it. The copy in the bootstrap seed modifies its replacement, and the replacement carries on from there. The provenance can still look normal.