This isn't, like, one misbehaving client. It's the way the ecosystem has evolved. GP didn't specify whether they were criticizing the standard or the ecosystem more broadly, but even if they were criticizing the standard, it's pretty fair to evaluate a standard at least partly based on how it gets implemented in practice. There's a reason cryptography tools for the last decade or more have been focused on being misuse-resistant.
Yes. I am criticizing the de facto web PKI, not the somewhat better design intent. The design intent is still bad though: we should never have given CAs universal issuance privileges.
The web has continued to go the wrong way in practice. (For example, browser makers rejected RFC9102 DNSSEC stapling, which could have enabled an incremental migration away from CA-centric hell.) Everything fix the existing web PKI community makes just seems to centralize trust more.
For example, Let's Encrypt has been useful for moving people off unencrypted services, but side it's now ubiquitous on the internet and had to work within the broken universal-grant CA model, it now represents a terrifying central point of failure. Had browser makers supported DANE instead, and had we embraced DNSSEC instead of casting aspersions on it, we wouldn't have needed Let's Encrypt because ownership of a domain name would have already, by that very fact, let you authenticate to anyone.
There is no one ecosystem. The world of web clients is highly diverse. Expecting every client implementation out there to converge onto one particular trust store is, first of all, magical thinking, but second of all, it reintroduces the single point of failure that web PKI is meant to avoid. The OS trust store is just one of many possible trust stores, there's nothing ordained about it. The problem is not with some standard, it's with a mistaken pre-conceived notion that there must only be one.
Many web clients have chosen to default to trust stores within their own ecosystem for usability and reproducibility reasons. When I as a user run "pip install requests", I expect to be able to issue HTTPS requests. I do not expect an implicit system dependency on ca-certificates - that might not even exist on my system!
If you want all of the web clients on your system to use a centrally managed trust store, then it's your responsibility to (a) know and enforce what clients exist on your system and (b) configure them all to use that trust store.