I think the article raises interesting questions about trust, but I am also doubtful if the definition of the “incoherent cryptosystem” is useful:

The article argues that Signal is an incoherent cryptosystem, because they ship the E2E-encrypting Signal client (and could, hence, backdoor it) that should protect me, the user, against their own infrastructure snooping on me.

As I understand the definition, we would not have an incoherent cryptosystem if I used a third-party client on Signal's infrastructure. Said Non-Signal client would implement E2E encryption, and use the Signal infrastructure, so the entity running the infrastructure is different from the entity providing the client. But is this any better?

Couldn't “Non-Signal Corp.” be coerced by the government (or decide to build a backdoor for their own gain) just as easily as “Signal”?

So I don't think it matters if the entity distributing the client is the same as the one running the infrastructure. It matters if I trust the client. How to implement this (audits, OSS, version pinning, ...) is still an open question to me.