It’s a really wicked problem to be sure. There is work underway in a bunch of places around different approaches to this; take a look at SBoM (software bill-of-materials) and reproducible builds. Doesn’t totally address the trust issue (the malicious xz releases had good gpg signatures from a trusted contributor), but makes it easier to spot binary tampering.
+1
Shameless plug to the OSS Review Toolkit project (https://oss-review-toolkit.org/ort/) which analyze your package manager, build a dependency tree and generates a SBOM for you. It can also check for vulnerabilitiea with the help of VulnerableCode.
It is mainly aimed at OSS Compliance though.
(I am a contributor)